Any enemy that heals or regenerates. You guys gave us a health bar, now abide by it. Enemies healing takes away all strategy, because you have no idea when it might heal again, and how long you'll have to fight it, and what do you do, do you conserve MP, what...?
Characters that are badass until you get them on your party. No, I want to use Magus' Dark Matter NOW. I don't want to wait for him to level up. He used it on me in the boss fight; what's your problem?
People dying in cutscenes when regeneration is possible in the ordinary game. You mean I've been getting burned, crushed, slashed, and otherwise beaten to a bloody death over and over, and one sword to the face is going to kill me in a cutscene? Excuse me?
I have a special place in my heart for Persona 3 and 4's tendency to do crap like not let you control your party members (P3), and killing your entire party when your main character dies. I HAVE REVIVES WHY CAN'T YOU USE THEM ON ME.
Baldur's Gate and Fallout 2 earned my hatred for having me miss all the time in combat. I'd rather do 1 damage every time, than miss half the time and then do 2 damage. It feels less like I was screwed over.
Unskippable cutscenes. Not being able to save whenever I want. Being able to take both sides in a morality meter (Mass Effect, I'm looking at you.) Always having to be either AMAZINGLY GOOD or AMAZINGLY EVIL to get interesting stuff. (Every other game with moral system, I'm now looking at you.)