Where do I even start... I'll do in order of campaigns, I guess.
Heleona:
* Being forced to walk everywhere in the beginning of Chapter 1, with lightning, sudden sounds and other trite horror movie clichés desperately trying (and failing) to scare you.
* The entirety of Chapter 3. Why was that needed again, other than to make sure the campaign has five chapters like the others?
* The entirety of Chapter 5. It's just one never-ending boss fight that gets more and more ridiculous with every stage, mixed with the occasional forcing-you-to-go-slow from the first chapter (this time in the form of an unskippable car ride with nothing to do).
Nivanfield:
* The Iluzija fight. Invisible enemies might be scary and/or challenging the first time you face them, but after that it just becomes tedious.
* The chopper fight where you first see Jake and Sherry in that chapter. The continuation on the rooftop is slightly less annoying.
* Honestly, the campaign as a whole. I like the military vibe, but other than that it's my least favourite campaign in terms of almost everything.
Shake:
* Chapter 2. Oh my Lucifer! From looking for tiny objects in a blizzard where one (literal) slip-up on the big ice slide forces you to restart from the bottom, to a shaky snowmobile section where one slip-up gets you killed immediately, to sneaking around in an ice cave where one slip-up has a 90% chance of getting you one-hit-drilled-to-death by Ustanak, to a button mashing contest where one slip-up... you get the idea. It's like someone in the development team thought, let's take everything that's annoying and put it in this one chapter!
* Playing as Sherry in general. Too much waiting around and watching Jake do the actual work (if he even bothers to do it at all; the AI never hits on the idea of taking out the chopper by climbing on to it), especially prominent in the fourth chapter and the final non-QTE confrontation with Ustanak. Also,
why did they need to have Jake hold her hand when she's about to deliver the killing blow to Ustanak on the moving platform, just so both players get to do something in this final QTE? Sherry being the one to kill it for good could have made up for her being virtually useless up until that point, but nope...
Agenda (thanks to
@Turo602 for pointing out that I shouldn't always ignore Agent!):
* "Speak into the microphone! Speak into the microphone!" ... How about
you speak into my butt?
* This is more related to story than gameplay, but the fact that Ada's third chapter begins and ends roughly around the same time as Nivanfield's, despite the latter taking like four times as long to complete, has always bothered me. Does Ada
actually walk everywhere in canon like the cutscenes suggest, or take an occasional nap here and there?
* Less frustrating and more awkward, but most of the "stealth" sections in the campaign. When a game that isn't otherwise suited for stealth gameplay suddenly tries to implement elements of it, that can only go one direction: Wrong!
The entire game:
* QTEs, full stop.
* Any encounter with the regenerating, self-mutilating, in-your-face-procreating I-don't-know-their-name-right-nows.