Mechanically, the most annoying thing for me is poor camera control because of a level or the environment. I'm a huge Dark Souls fan, and in a similar vein, have been playing Monster Hunter a lot lately. When I run into either boss fights, or monster fights, where the camera is all wonky due to the environment, usually tight surroundings, it drives me nuts, I'm looking at you Capra Demon. It's not something I feel I run into too often, but it drives me up a wall when it does.
Besides that I'd probably have to agree with poor platforming in games that don't need it, again usually 3D environments. I especially dislike it when its a case of, you have to make this jump, but there is very little indication as to how you make the jump or where, usually its, you will grab this ledge, but we aren't going to mark it in a way or make it in any way obvious that you are actually going to grab it, just jump and hope for the best.