Hopeless Boss Fights:
There is nothing more annoying than being beaten down by an enemy that's invincible but the game treats like an actual fight, especially if it's against an enemy you'd probably be able to and soon will beat with little trouble at all if they WEREN'T invincible (Calo Nord, I'm looking at YOU). Either make that enemy hard but beatable and have the plot go on like it's supposed to another way, (which I actually greatly like) or just have the protagonists get their asses handed to them in a cutscene instead, but not if it requires my next gripe.
Cutscene Incompetence:
Whether it be because the protagonists do something stupid no player with 2 brain cells to rub together would do if they were in control and that the protagonists themselves wouldn't do otherwise, surrender against paltry amounts of enemies the protagonists could easily kill by the score, or lose against a boss in a cutscene they'd be more than capable of taking otherwise, and so on the protagonist's abilities, intelligence, and just general competence in cutscenes should NOT be inversely proportional to that of those same characters when under the player's control, ESPECIALLY if even in other cutscenes they demonstrate far more competence than they do in those.
Advice for writers that might read this, if your plot requires something to be done outside of the player's control, let the protagonists be at least roughly as competent outside of that control as they are in it and build the plot around that. If the protagonists can take down dozens of mooks without breaking a sweat while the player is using them, don't bring in a handful of those same mooks to capture them and succeed, bring in some big guns the player isn't likely to be able to handle for another dozen hours or so. Don't have the protagonists act intelligent 99% of the time then have them doing suicidally stupid stuff and falling for painfully obvious traps that any 3 year old can see coming, at least TRY to pretend to be clever with how you get the protagonists into doing things, etc. YOU are writing the plot, it is YOU that decide to put these characters in situations, thus it is YOU who are responsible when you've written that plot into such a corner that there's nothing you can do but make those characters act much less competent in order to finish. YOU are God, rewrite the plot a bit and the characters until you find something that makes sense to what the player can do and the personalities of the characters. For instance, if you want the protagonists to be stupid enough to fall for a really really obvious trap, make a character that is stupid enough to fall for it (but not so stupid and not so many traps like this that they're doing this all the time and thus they become annoying) or make the trap it into something that would work on the character based on their personalities, goals, and what and who they care about. For instance, use a father's daughter as bait for the trap, and in a way said father doesn't have time and in too emotional a state to think or care about the trap.
Multiplayer focused or exclusive games:
To put it simply, NO game should require playing with other people in order to have any real value. ALL games that exist should be perfectly worth every penny solely on it's own merits without any human interaction whatsoever, that interaction should only be a bonus on top of that, not supplementing or entirely replacing it. This is especially true when it's online multiplayer and it requires players to shell out more money just to have access to it at all, subscription MMOs are easily the worst example of this. It's become an epidemic in the video game industry to shove multiplayer elements into games all the time especially ones that never needed it and thus are worse off or worse make entire games which have nothing BUT multiplayer to do and thus destroy any potential it could have had in the process (Yes, we're talking about YOU Star Wars Battlefront).
Turned Based Combat:
I'll just come right out and say it. I will live with it in indie and other low budget games where the money to make real time combat just isn't there, (and even that excuse won't hold up for very long as it continues to become cheaper and easier over the years) but in AAA RPGs at the very least there is absolutely NO reason turned based combat shouldn't be completely DEAD by now, including in remakes of old games that had it. Real time combat even done badly is vastly superior in every conceivable way to turned based combat, it's much much faster, more exciting, less tedious and especially much less limited than the latter and the former has been around for more than long enough to kill off the latter. It and the people that support turned based combat in this day and age is like deciding to go back to hunting tigers by bashing them with a stick and a rock like we used to back in the caveman days when we've got hunting rifles which work far far better and much more safely now and have for decades and then defending that decision at though that were possible.
This is especially true when it comes to the same ol "wait for a gauge to fill up, select from a list, watch as the characters do whatever you picked for the 20000th time without even further input", at least try to do like some turned based RPGs have done and add things like extra turns for performing well, timed hits, timed blocks/dodges, and that sort of thing. Skill should matter in games, but it's rare for a turned based game to have any more strategy required than "steamroll weaker enemies without hardly trying until you're strong enough to steamroll over stronger enemies without hardly trying, rinse and repeat," the Pokemon games are particularly bad about that. However, with real time combat you can NEVER get complacent because sometimes even enemies you were fighting regularly 10 hours ago can still lay you out if you don't watch yourself, (this usually means have some cheap move or instant death attack, but that's still better) and sometimes there are even rewards for playing well against those enemies even if they are total pushovers. Fighting itself should be enjoyable on it's own, not just be a means to an end and real time combat all but ensures that.