Overview:
In my opinion, there's too many perks in New Vegas that are either "automatic, default, I'm-going-to-get-this-every-playthrough-regardless-of-role-playing" perks, and the inverse, perks whose effects are so unappealing or niche or too far into the leveling scheme to be worth getting.
In addition, there's not enough emphasis on bonuses that are dynamic with SPECIAL skills, even though it's entirely possible based on the vanilla perk condition framework. They're generally used as requirements in the base game, but they don't generally affect perk bonuses, which is lame.

In complement to my Sweet 6 Shooter Perk Pack, this perk redux changes many perk bonuses to be SPECIAL proportional, many stat requirements have been reconfigured to be more balanced, immersive, or lore friendly. Some have been changed specifically to be less of an automatic decision. Many perk functions have been reconfigured entirely. Many perks whose bonuses have been converted to SPECIAL or Skill proportional have higher max bonus potential than their original values.

Any YUP changes and bugfixes have been considered and often included.

Strongly recommended for use with any mod which allows for unlimited traits.
I strongly recommend against use of any respec/trait removal mods, as well as the psych eval in OWB. They can cause issues with mod-added or altered perks, and I have no intention of trying to account for these circumstances. Extracurricular Knowledge in particular gets screwed up by it here.

When used with JAM and JBT Improved, the altered AP calculations for Math Wrath and VATS helper perk calculations will be correctly abided during Bullet Time.

Perk Changes:
Requirements which were altered listed below each perk.
Perks with changed effects or descriptions have their new description listed.

Steel Skeleton (Trait) [formerly Adamantium Skeleton]
Req: STR 4+
With the Steel Skeleton trait, your limbs only receive 75% of the damage they normally would, but your carry weight is reduced by 20%.

Action Boy/Girl have been entirely reworked into
Action Star
Req: Level 4, CHA 3+, AGI 5+
The life of an action star is an exciting one! As your career develops, you'll be able to choose to improve your total AP, your AP regeneration rate, or your weapon AP cost. If you take all three ranks, your AP is restored by (3 x Luck) on each headshot as well!
Headshot AP restoration does not occur during Bullet Time for balance reasons.

Alertness
Req: Level 2, INT 5+, PER 5+
This perk isn't very good, but it helps add choices in the early game and can synergize with other factors that care about Perception.

And Stay Back*
Req: Level 50, Guns 70+, Shotgun Surgeon
You've discovered a Shotgun technique that has a chance to knock an enemy back on any hits that penetrate the target's DT. Slugs have a much greater chance to cause knockdown.
(Requires that the hit penetrates DT, and it cannot perform a knockdown while the target is ragdolled or in the getting up animation. Slugs have an extra chance to perform a knockdown. The target's Strength, Endurance and armor class reduce the chance to be knocked down, and power armor cuts the knockdown chance in half.)

Animal Friend (Trait)
With the Animal Friend trait, animals come to your aid in combat, but never against another animal, and your weapon damage is reduced by 50% against animals, mutated animals, and mutated insects.
This would be a pretty automatic choice if it only affected animals and mutated animals, so I made it affect insects too. Have fun with the Cazadores ;D.

Ant Might
Your body has been genetically enhanced with the strength and flame resistance of the Grayditch Fire Ants! Your Strength has increased by 1 while sneaking, and you gain 3% resistance to fire per point in Endurance.
Extra strength while sneaking isn't amazing, but it's appropriate considering the stature of ants, and a raw SPECIAL bonus for this quest completion feels much too strong for its early game timing and easy quest.

Ant Sight
Your body has been genetically enhanced with the perception and flame resistance of the Grayditch Fire Ants! Your Perception has increased by 1 while sneaking, and you are gain 3% resistance to fire for each point in Endurance.
See Ant Might note.

Automatic Artistry (Previously Spray N Pray)
Req: Level 10, PER 4+
Automatic Artistry reduces your spread with automatic weapons by 15% and increases your crit. chance with them by 10%.
Spray N Pray was never particularly interesting, there aren't many perks affecting automatic weapons, and the icon fit, so I reworked it this way.

Avid Learner
Granted by completing 50 quests.

Better Criticals
With the Better Criticals perk, you gain a 3% critical damage bonus per point of Perception.
This is to make this perk more defined, and not an automatic choice for crit builds. Now you might actually consider getting something else instead if your perception isn't high.

Black Widow/Cherchez La Femme/Lady Killer/Confirmed Bachelor
Req: CHA 6+
+5 Speech and Barter and +1 Charisma when talking to preferred sex, but -5 Speech and Barter when talking to non-preferred sex.
These perks have trans support for both player selection and NPC detection - a small patch is available which provides an example of how to add the player or an NPC to the appropriate formlists.

Bloody Mess (Trait)
With the Bloody Mess trait, characters and creatures you kill will often explode into a red, gut-ridden, eyebalLevel strewn paste. Fun! Oh, and you gain +2% weapon damage per type of mutilated body part that you carry (Head, Arm, Leg, Organs, Torso).
However, your chance to set off mines, and enemy crit chance have been increased by 8%.

Broad Daylight
Req: Level 10, Sneak 50+
Added a sneak requirement cause it makes sense, and turned the level req waaay down, so that it can be more consequential throughout the game. It's bonus is just +15 Sneak, after all.

Built To Destroy
Req: AGI 4+
The Flamer that burns twice as bright burns half as long. Your weapon AP cost, throwing velocity, crit chance, equip, reload, attack, and aiming move speed are improved by 5%, but your spread is increased by 10%, and your weapon condition decays 20% faster.
Condition damage isn't a big deal without other mods enhancing it one way or another, so there wasn't much reason not to take it. Now it conveys a much more hectic handling of weapons.

Burden To Bear
Req: Level 16, STR 8+, END 8+, Strong Back
With the Burden To Bear perk, you can carry 4 more pounds of equipment for each point of both Strength and Endurance, on top of your Strong Back carry weight bonus.

Cannibal
Req: END 7+
With the Cannibal trait, when you're in Sneak mode, you gain the option to eat a corpse to regain Health equal to your Survival skill when your Hunger meets or exceeds your Survival skill. But every time you feed, you lose Karma, and if the act is witnessed, it is considered a crime against nature.
The hunger restoration has been altered from flat 25 to restoring a value equal to your survival skill. The radiation penalty has been increased to 25.

Careful Handling (Trait) [New]
Req: INT 4+, PER 4+
Your weapons deserve respect, and you know it. Your weapon AP cost, throwing velocity, equip, reload, and attack speed are reduced by 5%, but your spread and crit chance are improved by 5%, and your weapon condition decays 15% slower.
Inverse of Built To Destroy. Taking both will result in an overall reduction in stats with no benefit.

Center of Mass
Req: Energy Weapons 70+ or Guns 70+ or Big Guns 70+
You don't fool around with fancy trick shots. Straight to the midsection and down they go. In V.A.T.S., you do an additional 15% damage with attacks targeting the torso, and torso limb damage that you deal will be doubled.
This will help with staggering enemies by shooting for the torso.

Certified Tech
Req: Level 24, INT 5+, Repair 60+, Science 60+
A uselessly balanced and timed perk in vanilla. This configuration makes it more appealing. The odds and counts of the looted parts has been modified - it's no longer either zero parts or a bunch. The parts are more valuable than in vanilla.

Chem Resistant (Trait)
Req: END 7+
With the Chem Resistant trait, your addiction chance is reduced by 25%, but so is your chem duration.
Compatible with Overdose, whose use of this perk to increase the overdose threshold will still apply even with this change - it just won't be reflected in the description.
In vanilla, addictions don't have a duration. Use Sweet Healing Systems to have it actually affect addiction duration.

Child At Heart (Trait)
The Child at Heart trait greatly improves your interactions with children, usually in the form of unique dialogue choices, at the cost of -5 Speech when not speaking with a child.
Frankly, this thing still ain't great, but it's somewhat valuable for roleplay.

Claustrophobia
You have a fear of enclosed spaces. You gain +1 to SPECIAL attributes when outside, but suffer -1 when indoors.

Commando
Req: Level 12, PER 6+, Guns 60+ or Energy Weapons 60+ or Big Guns 40+
While using a rifle (or similar two-handed weapon), your accuracy is increased by 15% with each rank of the Commando perk.
Grants its accuracy bonus outside of VATS now, and has a second rank.

Comprehension
Disabled for being OP and substantially reducing the value of character building.

Computer Whiz
Granted by challenge after hacking 50 computers.

Concentrated Fire*
Req: Big Guns 60+ or Guns 60+ or Energy Weapons 60+
With Concentrated Fire, your accuracy when targeting any body part in V.A.T.S. increases slightly with each subsequent attack on that body part, and your spread is decreased by 20% when using an automatic weapon.
Similar to Automatic Artistry, but that perk just requires PER, and this one requires weapon skill.

Cowboy*
Req: Level 10, Melee Weapons 25+
When using any cowboy weapon, your attack speed, accuracy and damage are increased by 15%.
Shifts emphasis toward stylish and precise usage of cowboy weapons, and the DPS + damage boost is functionally higher than the vanilla damage boost if you're landing your hits.

Day Tripper 
You've done enough chems to know how to hang on to the effects just a while longer. Each point in Endurance grants you +3% chem duration.

Demolition Expert*
Req: Explosives 40+
With each rank of this perk, all of your Explosives weapons do an additional 10% damage and have 10% larger area of effect.
Only two ranks now.

Early Bird
You gain +1 to each of your SPECIAL attributes from 5 am to 12 pm, but suffer a -1 from 6 pm to 5 am when you're not at your best.
A 3 point disparity between ideal times and penalty times was too large, and it served to make you basically never do stuff outside those hours.

Educated
With the Educated trait, your book-smarts grant you a random free skill point every x level(s), but your Survival skill is reduced by 30, since you're not street-smart.
The stat requirement has been removed; you don't have to be smart to be educated. Level amount is configurable.

Entomologist
With the Entomologist perk, you do an additional +50% damage every time you attack a mutated insect, like the Radroach, Giant Mantis, or Radscorpion, and you are able to find more of their parts in loot.
Insect parts have only a 25% chance to drop without this perk.

Explorer
Granted by challenge for finding 125 locations.

Eye For An Eye
Req: Level 4, Luck 5+
While your head is crippled, you gain an additional 25% crit damage and crit chance.
The original effect was cute in its way, but a pain in the ass to actually do anything with. With this change, it's more specific to the head, and it may incentivize you to keep firing with a busted head instead of instantly doing something to heal it.

Fast Metabolism
Req: END 6+, Survival 25+
No free healing bonuses without a requirement.

Fast Shot
Req: AGI 6+
It also applies to Big Guns now.

Finesse
Req: AGI 5+
Can't have much finesse if you're clumsy.

Fortune Finder
Req: Luck 5+, Survival 35+

Friend of the Night
Req: PER 7+, Sneak 40+ or Survival 40+
Always good to make survival have more appeal.

Friendly Help
Your V.A.T.S. protectors will help you more often as your Luck increases.
Flat 2x likelihood in vanilla, now it's a stacking Luck bonus, 10% for each point. At 10 Luck, the bonus is 2.

Ghastly Scavenger
Req: END 8+
With Ghastly Scavenger, when you're in Sneak mode, you gain the option to eat a Super Mutant or Feral Ghoul corpse to regain Health. If this act is witnessed, it is considered a crime against nature.
No karma penalty anymore since I didn't see how it made much sense, health bonus is doubled to 50, hunger is restored by Survival x 2, radiation penalty jacked up to 50.

Good Natured
You're Good Natured at heart, more prone to solving problems with your mind than violence. You gain +1 to Charisma and +5 to Speech and Barter, but have -5 to Energy Weapons, Explosives, Guns, Melee Weapons, and Unarmed.
Simply getting to choose to boost all non-combat skills is just free skill points for characters which de-emphasize combat or only use one combat skill.

Good Natured also has a (near) inverse perk:
Rip N' Tear
Until it is done. Violence is the only way. You've gained +2 Strength and +5 Unarmed, but -2 to Charisma and -5 to Speech, Barter, Science, and Sneak.
Obviously these are not linear opposites. I've used mods that simply make an inversion of regular good natured for weapon skills, but having those two options just makes them default perks based on whether you want combat or non combat skills in the early game, since you can work off any deficit in a skill after a few levels with no issue. Now, they're more representative of character behavior types.

Grim Reaper's Sprint
Req: Level 14, Luck 6+
If you kill a target in V.A.T.S., 20 Action Points are restored upon exiting V.A.T.S. The second rank increases the amount to 60.
Full refill is too much. 20 is a decent reward for getting it at a much earlier level, and 60 is a solid restoration.

Grunt*
Req: Level 10, Guns 45+, Explosives 25+, Melee Weapons 20+
Just good, honest infantry work! When using U.S. army weapons, your explosives gain +15% damage, your automatic weapon spread is reduced by 20%, your semi-automatic spread is reduced by 10%, you gain +15% reload speed, and strength requirements are reduced by 1.
Increased the Explosives requirement to 25, and added a Melee Weapons 20 requirement, to tie it to the melee weapons that it applies to, and so that the Explosives requirement is as high as a basic frag grenade.
Additionally, the YUP/Sawyerbatty change to check for the guns skill for each bonus has been removed to allow it to work on melee/big guns/unarmed weapons, instead of excluding them. The automatic/semi auto weapons simply check if they're in the machineguns list or not.
I've genericized the weapon naming, and changed this perk from a raw damage upgrade to a wide selection of common guns, to instead be a substantial handling improvement, so that characters who are already happy with their handling may elect to skip this perk on a Guns run instead of always getting it.

Gunslinger
While using a one-handed weapon, your accuracy is increased by 15% per rank.
Has a second rank and applies outside of VATS now.

Hand Loader
Req: Level 12, Guns 50+ or Big Guns 50+
You know your way around a reloading bench and don't let good brass and hulls go to waste. When you use Guns, you are 50% more likely to recover cases and hulls. You also have access to advanced ammo types at the Reloading Bench. The second rank increases your chance to recover hulls by another 2x.

Heave Ho
Req: STR 5+ or AGI 6+, Explosives 25+ or Melee Weapons 25+
Quite an arm you've got there. All of your thrown weapons gain 25% velocity.
The vanilla velocity increase was often a liability instead of a benefit, since grenades bounce around like assholes at base speeds, let alone +50%.

Heavy Handed
Your melee and unarmed attacks do 20% more damage, but you attack 35% slower with them.
Req: AGI < 5
This made sense for any character that doesn't care about crits to take, so now it's an actual tradeoff that any character with a low enough Agility may consider.

Heavyweight
Req: Level 8, STR 7+ or END 7+
This perk has a very ambiguous appeal - the benefit that it offers will likely usually be less than that gained by carry weight increase perks, so I allowed it to be taken earlier and with Endurance as an option.

Hematophage
Instead of simply granting a small amount of extra Blood Pack healing, it now also grants a similar mechanic to Cannibal:
If you're outside of combat, crouched, with your weapon holstered, and targeting a dead adult human that hasn't been eaten with the Cannibal perk, you have the option to drink the NPC's blood.
This grants health, dehydration, and sleep deprivation restoration equal to the sum of your Endurance and Agility.
It damages your radiation by 18, but only reduces your karma by 25, instead of Cannibal's -100.
A sound and image effect plays when you drink blood, and it marks the corpse as eaten, so you can't go in twice with Cannibal.
It does not initiate hostility like Cannibal does, or play an animation. I don't really mind this much.
When used with only the NV file, this perk will be selectable in the levelup menu as of level 4, with an Endurance of 4+. When used with the TTW file, this perk will be hidden and granted via the Arefu quest as normal.

Here and Now
This perk never made logistical sense to take; it's been completely reworked as:
Extracurricular Knowledge
Selecting it will allow you to save a perk for later; at cost of being forced to take a trait. You can then use your stored perk point by simply highlighting the perk in your perk menu and hitting activate.

Hit The Deck
Req: Explosives 50+
Your familiarity with Explosives allows you to avoid a portion of their damage. Your Damage Threshold is increased by 15 against all Explosives.

Hoarder
You gain +20% carry weight, but suffer -1 to all SPECIAL stats when carrying less than 160 lbs.
+25 lbs was an atrociously underwhelming trade-off.

Hobbler
With the Hobbler perk, your attacks to legs deal double limb damage, your run speed is increased by 10% with each crippled leg, and you gain +5 DT penetration and 25% better chance to hit an opponent's legs in V.A.T.S.
It's tough to incentivize not shooting for the head in most circumstances, so this is very powerful to make doing so appealing.

Home On The Range
Req: Level 6, Survival 35+
This change was made with the expectation that you have some sort of mod like Sweet Healing Systems that reduces or removes sleep healing.

Hot Blooded
Req: AGI 4+
When your health drops below 50%, your attack speed is increased by 25%, but your weapon condition damage is doubled.
The original setup for this trait was... weird. Why would it reduce Agility?

Hunter
Req: PER 6+, Survival 30+
In combat, you do +50% Critical Damage against animals and mutated animals, and +50% damage against them while using Guns and sneaking. You're also able to collect their meat.
25% animal loot drops without this perk.

In Shining Armor
Req: Level 2, Repair 40+, Science 30+
Beams reflect off the mirror-like finish of your gleaming armor! You gain an additional +5 Damage Threshold against energy weapons while wearing any metal armor, and +2 while wearing reflective eyewear.
Another fairly niche perk, so I reduced its requirements dramatically.

Infiltrator
Granted by picking 100 locks.

Irradiated Beauty
Req: Level 6, CHA 4+, END 6+
When doused in radiation, your natural aura is enhanced. You gain +1 Charisma at 250/450/650 rads.
The game should have more perks that give bonuses for having rads.

Jury Rigging
Req: Level 24, Repair 90+, INT 7+
A very powerful economic tool, so I've made it tougher to get.

Kamikaze
Req: INT < 5
You gain +25% run speed while in combat and below 50% health, but you also have -5 DT while those conditions are met.
Different bonus than Hot Blooded, same circumstances. Added a low INT req to differentiate it a touch more.

Laser Commander*
Req: Level 18, Energy Weapons 75+
This thing's pretty good, but getting it earlier in the game would make it more appealing to stick with lasers instead of swapping up to gauss or plasma.

Lead Belly
Req: Level 2, Survival 40+ or END 7+
With each rank of the Lead Belly perk, you take 25% less radiation when consuming irradiated food and drink.

Life Giver
With the Life Giver perk, you and your companions gain an additional 30 health.
The Endurance requirement has been removed, since this perk would be most appealing to low Endurance characters, rather than high ones, and there isn't necessarily anything about the icon or flavor text that would imply an Endurance necessity.

Light Step 
Req: Level 6, Sneak 40+
With the Light Step perk, your chance to set off mines and floor-based traps while sneaking is reduced by 10% per point of Agility. This effect is multiplicative, with a minimum chance to set off traps of 35%.
Why didn't this require sneak in the first place? Having this be a binary on/off switch was also lame as fuck and fairly unimmersive. These changes shift the focus to stealth characters, and incentivize still taking the time to be careful with traps instead of just running over them like someone who knows they can magically not set off mines.

Light Touch
Heavy armor just isn't your thing, so you've learned to customize light armor for maximum benefit. While wearing light armor or clothing, you gain +3 DT and DR, and your enemies suffer a -25% Critical Hit Chance.
Req: Level 6, AGI 6+, STR < 6
This perk sucked before.

Living Anatomy
Req: Level 12
Living Anatomy allows you to see the Health and Damage Threshold of any target. It also gives you a +5% bonus to damage against Humans and non-feral Ghouls, and allows you to collect resources from abominations.
25% chance for abomination loot without this perk.

Long Haul 
Req: END 8+
The base game had an issue with making Barter a requirement for perks which enhance Barter builds, but don't actually thematically relate to the nature of their bonus at all. The Endurance req is much higher, but it doesn't require Barter nonsensically anymore. The high END req is justified by how much an infinite carry weight for the sake of fast travel affects game economy.

Loose Cannon 
Req: AGI 6+ or STR 5+

Marathon Runner
Req: Level 10
Your run speed is increased by 20% while wearing nothing, 15% while wearing light armor, 10% while wearing medium armor, and 5% while wearing heavy armor.
The level 4 requirement made sense with the previous bonus amount and its specificity to light armor, but with the boosted bonus and broader appeal, I increased the level requirement.

Math Wrath
Req: Level 14, Science 70+ or INT 8+
You are able to optimize your Pip-Boy's V.A.T.S. logic, reducing all AP costs by 5% per each 10 points in Science above 40.
10% was pretty underwhelming.

Meltdown
Meltdown causes foes killed by your plasma weapons to give off a corona of harmful energy. You also gain +25% crit. damage with plasma weapons.
This perk really needed another bonus to compensate for how dangerous it is to the user. The original chain explosion effect can be toggled on or off in the config ini.

Mile In Their Shoes
Disabled for being far too niche.

Miss Fortune and Mysterious Stranger are now traits. The former reduces your Luck by 1, and the latter reduces your crit. chance by 15%.

Mister Sandman 
Req: Level 6, Sneak 50+, AGI 8+
Pretty rare use case, but a free, silent kill that disregards the target's health, armor, etc. is pretty strong.

Nerd Rage
You've been pushed around long enough! Whenever your health drops below 20%, enemy crit. chance is reduced by 10% for each point of Intelligence you have.
Req: Science 75+
I always thought this perk was too appealing to all builds, and that it didn't feel like it made a ton of sense. I removed the INT req cause anyone can be a nerd, regardless of intellect.

Nerves of Steel
With the Nerves of Steel perk, you regenerate Action Points 20% faster per rank.
Req: AGI 6+, END 4+
Vanilla bonus was still 20%, I just added a second rank.

Night Person (Trait)
When the sun is down, a Night Person gains +1 to both Intelligence and Perception.
Req: PER 4+, no Solar Powered
Always sounded like a personal trait and not a skill that one develops. Excluded it from Solar Powered for theming.

Ninja
Req: Sneak 80+, Melee Weapons or Unarmed 80+
It offered Unarmed bonuses, but couldn't be obtained via Unarmed?

Nuka Chemist
Req: Level 14, Science 65+
The Nuka-Quantum recipe previously only available via Quantum Chemist has been made available with this perk instead.
There was no reason for this perk to have such high requirements.

Old World Gourmet
Req: Level 2

Pack Rat
Req: Level 30, Survival 80+, INT 6+
This perk has a huge effect on the economy. Its Barter req didn't make much sense either. Now you can either shoot for this as a late game economy boost for Survival characters, or cross-build Barter and Survival to get a substantial economy momentum boost in the mid/late-ish game.

Paralyzing Palm
Granted by dealing 25000 Unarmed damage.

Piercing Strike
Req: STR 7+, Unarmed 50+ or Melee Weapons 50
Piercing Strike makes all of your Unarmed and Melee Weapons (including thrown) negate 2 points of Damage Threshold on the target per point in Strength.

Plasma Spaz*
You're just so excited about plasma that you can't (magnetically) contain yourself! Your attack speed and AP cost with plasma weapons are improved by 20%.

Quick Draw
Quick Draw makes all of your weapon equipping and holstering 10% faster per each 10 points in the appropriate weapon skill above 30.
Appropriate weapon skill means that if you're using Guns, it checks for Guns, etc. Big Guns are covered.

Rad Absorption
Req: Level 14, END 7+ or Survival 50+
With the Rad Absorption perk, your radiation level dissipates by 1 point every 10 seconds.
Dissipates twice as fast as vanilla. Still not particularly strong, so I reduced its level requirement and allowed for Survival to acquire it.

Rapid Reload 
Req: Level 8, AGI 5+, Guns 40+ or Energy Weapons 40+ or Big Guns 40+
Rapid Reload makes all of your weapon reloads 15% faster.
The biggest issue with this perk in vanilla is that it made the reload animations look really dumb, so I toned it down a bit. Level 2 was also really early in my opinion.

Retention
Req: INT 6+

Robotics Expert
Req: Science 50+, INT 5+
With the Robotics Expert perk, you do an additional 7% damage per 10 points in Science above 50 to robots. In addition, activating a hostile robot while undetected will allow you to put that robot into a permanent shutdown state.

Roughin' It
Req: Level 2, Survival 25+
This bonus sucks. The TTW patch hides it, as it overlaps with Deep Sleep but without as much appeal as that perk. I've left it in for NV players, but I strongly considered hiding it in general.

Run N' Gun 
Req: Level 8, Guns 45+ or Energy Weapons 45+ or Big Guns 45

Scrounger
Req: Survival 50+, Luck 3
More about Survival and less about Luck than Fortune Finder.

Talented (formerly Skilled)
You're talented, but a slow learner. You gain +5 points to every skill, but you suffer -1/2/3/4/5 (configurable) gained skill points per level.
This was originally an overwhelmingly positive trait to take, especially in the context of TTW's wildly increased opportunities for XP. Now it's a substantial boost to early game skill checks and such, at a potentially large loss of total skill points by max level. This value can be changed between -1/-2/-3 skill points - 3 is recommended for a level cap of ~30, like many Sawyer style mods implement, while 2 is recommended for TTW's default level cap of 60.
+5 to each skill = +70 skill points w/ Big Guns, +65 without
3 * 30 = -90 skill points
2 * 60 = -120 skill points
TTW's horde of skill books offsets the extra penalty IMO

Shotgun Surgeon*
Req: Level 10, PER 6+
Your precision with a scattergun is something to behold. When using shotguns, each rank of Shotgun Surgeon grants you 6 points of Damage Threshold penetration and -8% spread.

Silent Running
Req: Level 6
With the Silent Running perk, running no longer factors into a successful sneak attempt. The second rank grants an additional +2% sneaking speed per each 10 points in Sneak.
Having to toggle walk or hold the stick halfway sucks. I almost want to provide this to all characters globally, but I've managed to restrain myself from doing so.

Slayer
Req: Level 20, AGI 7+, STR 7+, Unarmed 70+ or Melee Weapons 70+
The slayer walks the earth! Each rank of the Slayer perk increases the speed of all your Melee Weapons and Unarmed attacks by 20%.
This thing's requirements demanding Unarmed was dumb.

Small Frame
Due to your small size, you have +15 Sneak, and are 15% harder to detect while sneaking, but you also suffer -1 Endurance and Strength.

Sneering Imperialist
Req: Evil or Very Evil
You don't take kindly to raiders, junkies, or tribals trying to "settle" or "stay alive" in civilized lands. Against dirty raider, slaver and junkie types, as well as tribals, you do +15% damage and have a bonus to hit in V.A.T.S.

Sniper
Req: Level 28, PER 8+, Guns 75+ or Energy Weapons 75+ or Big Guns 75+
With the Sniper perk, your chance to hit an opponent's head in V.A.T.S. is increased by 25%, and your crit. chance is increased by 25% while using a scope and crouched.
The crit. chance bonus is for once you're no longer undetected.

Solar Powered (Trait)
No Night Person.
With the Solar Powered trait, you gain an additional point in Strength, Agility, and Endurance while in sunlight, but you suffer -1 to these stats while indoors or during the night.

Splash Damage
Req: Explosives 60+

Splash Damage and Demolitions Expert have been changed to check for the demo expert formlist, instead of explosives skill, for better compatibility with Big Guns mods.

Stonewall
Req: STR 7+ and END 7+
You gain +1 Damage Threshold against all Melee Weapons and Unarmed attacks per point in Endurance, and immunity to knockdowns.
Immunity to knockdowns is quite strong, so I increased the reqs.

Strong Back
Req: Level 6, END 6+ and STR 6+
With the Strong Back perk, you can carry 4 more pounds of equipment for each point of both Strength and Endurance, up to a maximum of +80 lbs.

Super Slam
Req: Level 12, Melee Weapons 55+ or Unarmed 55+
All Melee Weapons and Unarmed attacks have a chance to knock your target down when they penetrate the target's DT. This chance increases based on weapon weight and power attacking, and is proportionally reduced when a weapon's strength requirement is not met.
Throwing weapons of all types do count now; however, since weapon weight is a big factor in the calculation, light throwing weapons are very unlikely to cause knockdown.
(Requires that the hit penetrates DT, and it cannot perform a knockdown while the target is ragdolled or in the getting up animation. The target's Strength, Endurance and armor class reduce the chance to be knocked down, and power armor cuts the knockdown chance in half. Automatic melee weapons are prohibited from knockdown.)

Swift Learner
Req: INT 4+ and PER 4+
The Swift Learner perk grants an additional 2% gained XP per point in Intelligence.

Terrifying Presence (Trait)
Req: CHA < 5
In some conversations, you gain the ability to initiate combat while terrifying your opponents, sending them fleeing away for safety. Your enemy's crit. chance is also reduced by 5% for each point that your Charisma is below 5, but you suffer -1 Charisma and -5 Speech.

Them's Good Eatin'
Req: Level 8, Survival 75+
You've gained a chance to find a Thin Red Paste or Blood Sausage when looting any animal.
Generally expects food healing to be nerfed to some degree, but with those items still being pretty good. The change to just animals helps keep you from overflowing with those items like in vanilla.

The Professional*
Req: Sneak 50+
20% is a rather small bonus to be getting compared to the 2x from sneak crits for the high req. of 75 skill.

Toughness
Req: Level 8
With the Toughness perk, you gain +1 Damage Threshold per point in Endurance.
(Vanilla UI Plus has a strange behavior, where if you hover over an aid item then move the cursor/highlighted item, the DR part of the pip boy ui won't show the correct value if you have the Toughness perk).

Tribal Ways (formerly Tribal Wisdom)*
Req: Level 4, END 6+, Survival 50+
Your limbs take 50% less damage from Animals, Mutated Animals, and Mutated Insects, and you gain +20% damage and attack speed with tribal weapons, as well as +8 DT, +25% DR, and +10% run speed while wearing a tribal outfit. [Weapons image 1] [Weapons image 2]
There aren't any perks for tribal weapons and such for roleplaying or character development, and the limb damage wasn't very appealing. The weapons and armors covered aren't very strong, so this is made fairly easy to get in the early game.

Trigger Discipline
Req: INT 4+
While using Guns, Energy Weapons, or Big Guns, you fire 20% more slowly, but your spread is reduced by 20%.

Tunnel Runner
Req: Level 8
It's invaluable to keep your head down. Your movement speed is increased by 25% while sneaking in light armor with your weapon holstered.

Unstoppable Force
Req: STR 7, Unarmed 60+ or Melee Weapons 60+
Your martial might is truly legendary. You do 4x damage through enemy blocks with all Melee Weapons and Unarmed attacks while moving forward.
This perk is also granted by the "Were You Using That" challenge for crippling enemy limbs with two handed melee weapons. I could have hidden it, but I left it selectable in case you're an unarmed character that really wants the perk.
YUP added the requirement that you're moving forward for this perk's effect, which has been maintained and clarified in the description.

Vigilant Recycler
Req: Science 70+, Energy Weapons 50+

Voracious Reader 
Disabled for being niche and awkwardly implemented.

Walker Instinct
Req: Level 2, Survival 35+, PER 3+
Your senses have become so keen that you can feel the slightest vibration in the ground. You gain +1 Perception and Agility attributes while outside and crouched.
This perk sucked before, and it still sucks. Being available at an earlier level helps it have some modicum of appeal.

Weapon Handling
Req: Level 12, END 5+
You've become more accustomed to handling heavy weaponry. The Weapon Handling perk reduces weapon Strength requirements by 1 each when you reach levels 66 and 99 of your equipped weapon skill.

Companion Changes:
Companion perk texts have been altered to say "you" instead of "the player."

Full Maintenance only reduces item damage by 25%.
Too OP before.

Intellectual Assessment (formerly Better Healing)
While Arcade is a companion, you gain +7 to Science and +1 to Intelligence.
Arcade's not a doctor.

Over-Compensation
Bonus reduced to -1 Strength requirement, as 2 was too strong.

Second Skin
Star Paladin Cross is a seasoned veteran of power armor use and can show you a thing or two about how to use it at it's maximum potential. While Star Paladin Cross is in your party, you have +1 Endurance and +20 carry weight when you are wearing power armor.

OWB Changes:
The OWB perks were OP, considering that you always get three just for showing up in Big MT. There's also an issue, in my opinion, with the "choice" presented in OWB between leaving the Think Tank alive or not: there's no real reason to kill them unless you just abjectly haven't done a bunch of the stuff in the DLC.
I want you to have more reasons for the player to potentially want to kill them, so the body part perks have been totally revamped, in order to debuff you, for balance, as well as to make you more unhappy with the Think Tank and what they've done to your body.
The perks for when your original parts are reinstalled generally don't have debuffs, but their bonuses are often substantially weaker.

Big Brained
Your brain is back in your body, but some of the advanced technologies remain: Your head can be crippled again, but you are still 35% more resistant to addiction, and you gain +1 Intelligence and +10% XP.
Brainless
Your brain has been replaced with advanced technologies: Your head can no longer be crippled, and your addiction chance is removed, but your radiation intake while drinking is doubled, and you have -1 Perception.

Heartless
Your heart has been replaced with advanced technologies: You cannot be poisoned, and your AP regen speed has increased by 25%, but your recovered health is reduced by 25%, your max health has been reduced by 50, and your radiation resistance has been reduced by 25%.
Cardiac Arrest
Your heart is back in your body, but some advanced technologies remain: You still suffer -15 radiation resistance, but your health and AP have increased by 25, and your damage resistance has increased by 5%.

Spineless
Your spine has been replaced with advanced technologies: Your torso can no longer be crippled, and your carry weight has increased by 25%, but your attack speed with Unarmed, and Melee Weapons has been reduced by 25%, and your equip speed has been reduced by 25%.
Reinforced Spine
Your spine is back in your body, but some advanced technologies remain: Your torso can be crippled again, but you've gained +1 Endurance and +2 DT.

DNAgent
Studying schematics on the abominations created at the Big MT has granted you a damage bonus (+10%) against Abominations.
Just nightstalkers made this perk very niche and not worth the money.
Implant C-13
Implant C-13 is a defense turret subroutine that has been modified for implantation into humans. It enhances accuracy and damage dealt against targets in the air by 10%.
Still applies to cazadores, but it has a broader appeal now.
Implant Y-3 
Implant Y-3 places an internal filtration system in the digestive tract that strips any liquid consumed of all* radioactive particles.*Within standard tolerance levels
6% drinking radiation instead of 1%.
Implant M-5
You can be made... better... faster... stronger... Actually, just faster. The M-5 implant increases your crouched movement speed by 10% for greater efficiency as a test subject.
There's a lot of chances for sneak speed boosts in the game, so I nerfed this from 20 to 10%.

Lonesome Road:
Oderint Dum Metuant (The Bear-Slayer)
You've set the toothless NCR ablaze with that most unholy of powers, nuclear fusion. While facing members of the NCR, you penetrate 8 DT, and deal 15% more damage with guns and flame-based weapons while your karma is Bad or Very Bad.
Igne Natura Renovatur Integra (Dead Man's Burden)
200 years after the Great War, two lone nuclear missiles were launched. Not aimed at another country, but at their own land, targeting the last vestiges of civilization, a wicked punishment for their audacity to grow and thrive in this desolate wasteland. You deal +20% damage and +10% critical damage when attacking any members of the NCR or Legion while your karma is Bad or Very Bad.
Non Ducor, Duco (Divide Survivor)
Though neither the NCR or the Legion is a perfect solution for the Mojave, neither is worth damaging at the cost of repeating humanity's greatest sin. You've gain +1 Intelligence, Charisma, and Luck while your karma is Good or Very Good.
Sic Semper Tyrannis (Scourge of the East)
You've set the tyrannical Legion ablaze with that most unholy of powers, nuclear fusion. While facing members of the Legion, you penetrate 8 DT, and deal 15% more damage with melee and flame-based weapons while your karma is Evil or Very Evil.

Just Lucky I'm Alive
You've had lots of close calls. Whenever you finish a fight with less than 25% Health, your Luck increases by +4 for 3 minutes. You're also -25% as likely to be critically hit, and your own critical hits inflict +25% damage. (Requires Neutral Karma.)
Ain't Like That Now
Maybe you were bad once, but you ain't like that now. Your Karma has been reset, you regenerate AP 20% faster, and your attack speed is increased by 20%. You are also 25% less susceptible to critical hits from Evil or Very Evil characters. (Requires Bad Karma.)
Thought You Died
Your storied past has fallen from memory 'cause everyone thought you died. Your Karma is reset, you inflict +15% damage against Evil or Very Evil characters, as well as being 25% less susceptible to their critical hits, and you gain +50 Health. (Requires Good Karma.)

Marked has had a YUP bug that caused the DT bonus to not work; it's been fixed here so that it'll actually work again.

TTW Side:
Use with the main file.
PLACE THE TTW FILE BELOW THE NV FILE

Almost Perfect and No Weaknesses have been hidden; they were OP and broke stuff with BHYSYS.

Auto Axpert
You've become an expert with the Auto Axe. Its Strength requirement has been reduced by 1, and you deal +15% damage with all automatic melee weapons.

Barter Town
Bonus nerfed from 10% at each rank to 2/6/12%

Contract Killer
Req: Evil or Very Evil.

Cyborg
Req: Level 14
34 was an absurd level for a small amount of a couple resistances,

Daddy's Boy/Girl
Req: INT 6+
Just like dear old Dad, you've devoted your time to intellectual pursuits. With each rank, hacking gets easier and you use chems 10% more effectively.

Deep Sleep
Req: Level 6, Survival 30+
This perk sucks. Being at a low level helps, but this bonus is terrible.

Dream Crusher
Something about your presence dampens others' desires to exceed. Your enemy's chance of getting critical hits on you is multiplied by .1 for each point your Charisma is below 10 based on how low your Charisma is below 10.

Escalator to Heaven/Devil'sHighway/Karmic Rebalance
Disabled. These only had value back in F3, which didn't have very many perks.

Gun Nut
Req: INT 4+, Repair 30+, Guns 30+
You're obsessed with using and maintaining a wide variety of conventional firearms. With each rank of the Gun Nut perk, when using a gun, spread and item condition damage are reduced by 5%.
Why didn't this require Repair originally??

Impartial Mediation (Trait)
With the Impartial Mediation trait, you gain +10 points to Speech while you maintain a neutral karma level, but you suffer -1 Charisma and -5 Speech while Good, Very Good, Evil, or Very Evil.

Iron Fist
Req: STR 4+, END 5+, Unarmed 25+
With each rank of the Iron Fist perk, you deal +1 Unarmed damage per rank of Endurance.
Only two ranks.

Lawbringer
Req: Good or Very Good

Little Leaguer
Req: STR 4+, Melee Weapons 25+
Years as the Vault little league MVP have honed your hitting and throwing. With each rank, you gain 10% damage when using bats and nail boards, and you throw grenades 10% harder and farther.

Master Trader
Req: Level 26, CHA 7+, Barter 50+ and Speech 50+
When you take the Master Trader perk, you gain a 3% discount per 10 points in Speech.

Nuclear Anomaly
Req: END 10+

Party Boy/Girl
Disabled.

Puppies
Req: Level 2, Luck 8+

Quantum Chemist 
Disabled. This overlapped with whatever that other Nuka-Chemist and the recipe for it has been made available with that perk instead.

Rad Tolerance
Disabled. Clumsy implementation, since the message still shows and such. Not worth bothering to keep.

Scoundrel
Req: CHA 7+, Evil or Very Evil
Take the Scoundrel perk, and you can use your wily charms to influence people. With each rank, vendors give an 8% discount, and you gain and extra XP for passing speech checks.

Size Matters
You're obsessed with really big weapons. With each rank of this perk, you gain 10% better accuracy, reload and equip speed when using Big Guns.
Req: Level 4, STR 5+, Big Guns 30+
This is the only perk affected by the No Big Guns patch, since it's the only one that outright requires BG instead of just having it as an option. The effects have been changed to apply to anything in the TTW big guns list as well as anything that directly uses BG.

Staunch Defender
Renamed from Superior Defender.
With the Staunch Defender Perk, you gain +5 DT while standing still in combat.
A flat +5 damage is a confounding factor in weapon damage balancing, but its removal is offset by the DT change, which is more useful than DR.

Swing for the Fences
Req: Level 2, STR 6+
Knock em right outta the park! Your attack speed with two handed melee weapons is increased by 8%, and you do an additional 7 points of damage while using any baseball bat.

Thief
With each rank of the Thief perk, you +5 Sneak and +5% pickpocket chance.
Loooottttaaa sneak speed bonuses out there, so I changed it to a sneak bonus.

Challenge Changes:
Challenge perks whose text has been genericized:
Format: You've gained a damage bonus against ___.
Abominable
Animal Control
Mutant Massacre
Machine Head
The flavor text on these wasn't clever or charming enough to justify the meta-textual references.

Beautiful Beatdown
Your Unarmed weapon AP Cost is reduced by 20%.

Melee Hacker has been renamed to Hack N' Slash.

Destroy Something Not So Beautiful has been changed to Knockout Punch, and it grants Paralyzing Palm, in addition to the regular challenge perk.

Perks marked with a * can be right/left clicked or press "grab" while they're selected in the Pip-Boy Stats->Perks menu or leveLevel up perk menu. In the Pip-Boy, his will display a pop-up, offering to show you the qualifying items. (Shotgun weapons, grunt weapon, tribal armors/weapons, etc.) In the perk menu, it will immediately show the items without a prompt.

Requirements:
JIP LN and Johnny Guitar are required.

Installation:
Regular installation.
TTW users should download the TTW file listed in the optional files.
PLACE THE TTW FILE BELOW THE NV FILE IF YOU'RE USING IT

As of version 13, The Way - A Small Trait Mod has been broken up and included here and my Base Game Perks Redux. Delete that file if you have it.
As you should be able to intuit, both of these files belong below any bugfixing mods or anything else that touches perks.

Compatible with 3.3+

Credits:
bigcman123 for the Vault Girl face icon used in the promo image.
ItsMeJesusHChrist's V4 CPI icons were used for the upscaled icons used in the promo image, as well as the V4 CPI initial resources used for a couple of custom icons.
cdr for Perk Based Creature Loot

Support:
If you'd like to support my modding work or say thanks, feel free to donate via the Nexus or here at Ko-Fi.