It seems to have popped up in this thread alot, but mine is also time limits, Dead Rising is the first to come to mind, that game would have been awesome, but then they decided to make you rush everywhere so you can't enjoy any of it.
Also degenerating health, most recent is Lost Planet I think, but that isn't really an issue as most game companies know this is a fucking stupid idea.
Now that I think about it, my answer is Capcom, they just suck at making games, they have these great concepts for games, then ruin them by adding these stupid little quirks:
Resident Evil - The aiming and save system
Dead Rising - The aiming, save system and time limit
Lost Planet - Degenerating health
Devil May Cry - That stupid arse score system, fuck you giving me a D, I completed the level...bastard.
So yeah, any game made by Capcom is bound to have a design flaw I hate.