Artificial light reflections. It was cool the first time I saw one (I think Sonic Adventure), but Christ what an annoyance! And so many games have them. Why? If I never see another light relfection in a game, it'll be too soon.
What about the reliance upon the analog stick for primary control? Since 1985 (or so) when the NES was first released, the directional cross has proved optimal for character control. Some will no doubt disagree, as analog makes it easier to move fast or slow, but whatever happened to the days when you used the d cross and pushed a button while moving to run/sneak/etc.? Isn't that much easier than not knowing precisely how much pressure to use and accidentally making your character walk when he's supposed to tiptoe past an enemy?
Graphical pop-in. Man, this is getting out of hand. I can't tell you how many times I have been flying my helicopter/airplane in San Andreas, only to crash into a tree that wasn't there a second ago!
The analog stick/buttons are also a nuisance. In the above-mentioned game, I was just about to finish my 11th of 12 Firefighter missions when using the right analog stick to move the water nozzle, I accidentally pushed R3, cancelling the whole God damned mission! L3 and R3 are lousily placed buttons, and the whole concept of pushing down on a stick sucks.
Any others you'd care to mention?