I have a lot... here goes.
The Brick Bossfight - You know the one, where some big large heavy indestructible boss charges at you for a couple of rounds then bangs his head on some piece of the scenery and you have a couple of seconds to wail in on him with relative impunity before he gets back up and repeats the process 2 or 3 more times... Yeah I'm getting real sick of this boss formula.
Time-Saver DLCs - Their very existence suggests that the dev put pointless annoying NOT FUN repetitive tasks in the game to try to sucker you into these things to progress past them.
Inventory Stack Limits WITH Inventory Weight Limits - I get the point of a stack limit, to show there's some kind of limit to how much your character can carry, but when you also have weight limits, having a stack limit also just is irritating...
No-Confirmation Cutscene Skips - Moreso than unskippable cutscenes I hate when I'm either not expecting a cutscene or I accidentally press a button and suddenly I've skipped the whole thing and now I have no clue at all what just happened! Give me a cutscene skip option but please don't tie it to my primary action buttons, or at least ask me "Are you sure?" first
In-game DLC or Online Content reminders - I hate having guys in my camp in Dragon's Age telling me I can go on an awesome adventure... if I buy a DLC... or my ship cabin in AC4 telling me I need to be online to use this feature... it's so immersion breaking.
Modern RPGs that don't show equipment changes on your characters - I can forgive this well enough for any game pre-2000, but it's gotten to the point where status quo says if you upgrade from a leather jerkin to iron armor you should have something to indicate that your character is at least now wearing a shirt.
No Body Sliders in Character Creators - I appreciate the 500+ options to fine-tune my character's face but why can't I so much as alter their height or basic build? Outside of Saints Row 2/3 and The Sims I've rarely seen any sort of options for modifying your character's body, we're not all cookie cutter you know! Maybe I want my heroes pudgy or at least not looking like Arnold Scwarzenegger in his prime.
Tactical RPGs on Flat Maps - Final Fantasy Tactics came out in 1997, over 15 years later we're still getting tactical RPGs that can't top that. The biggest pet peeve are completely flat maps with no height terrain or obstacles, that's just booooring!
No Jump Button - Baldur's Gate Dark Alliance was wonderful enough to give us a jump button and absolutely zero use for it whatsoever (save that one spot where you could jump on crates to get to a chest) but it was there! I don't expect devs to add clever uses for a jump mechanic in their game, but just the ability to jump somehow improves your game by a nominal margin!
Last of all, this isn't actually a "game" pet peeve but:
When the cost of all DLC is more than the game + all DLC - I can't stand it when I see a GOTY or Ultimate Edition of a game I already own for like 7$ and if I just want to buy all the DLC for that game I have to pay 12.50$... admittedly this seems to be more of a Steam issue than anything but... yeah.