Imprecise control: every interact input is contextual, and if there are multiple interactables close together it's pretty much random which one will be selected when you first approach.
Unreliable/unclear mechanics: sometimes you shoot a guy with a big gun and the guys one floor above don't hear a thing, another time you kill the same guy by swinging a hammer at him and half the map hears it, also most guns have too much spread to consistently land headshots even at half a screen's width.
Lack of mid-level checkpoints plus very cheap tricks: if you played the "Forced Conversion" level you know how ridiculous that can get.
Questionable balancing: you don't get enough souls to purchase all available weapons, not that it matters since there's only 2-3 that are worth buying.
A general smattering of bugs: double primary glitch, vent exploits, a variety of mission objectives being actually optional if you just walk to the next objective...
And worst of all, there's no depth to it: just go fast, enemy wakeup times are so much more lenient than everything else so 99% of the encounters can be solved by running in and spraying shots at head height, hell even your score is determined almost exclusively by clear time (technically accuracy and headshot % also matter, but only if they sum up to more than 150% and even then the bonus is tiny).

Ah, and the "Get all other achievements" achievement is actually the "Get all the other achievements IN A SINGLE SAVE FILE" achievement, which is just silly.