Yeah... that's another thing I hate, is bosses that are too easy. I just played Doom 3... the last boss? A joke! How anticlimactic! Just run in a circle and you're good to go. Not that this is new to Doom... it's not that hard to get the BFG before the end of episode 3, or again before 4 (which was not added until later, but still...). Just fire off a few shots with it, and you win. If you had it when you fought the cyberdemon, he'd probably be easy, too. These are certainly not the only games that have this problem, but these are good examples. Easy bosses strike me as poor game design.
How about poorly implemented checkpoints? CoD2 pissed me off, because not only did it have another damn Normandy beach level, but the checkpoints felt like they were 90 miles apart. I found myself wondering "Where's the next one, Berlin?" Checkpoints are tolerable or even sensible in some games, but games where you can die easily would be better with quicksaves instead, or in addition. When you have to redo the same crap ten times over, something's wrong, and it's probably not your fault...
I also dislike games that force me to do something which seems out of context with the rest of the game... not sure how to explain just what I mean... the Simon thing is just one example... I think a good example is the part in GTA:VC where you have to race that guy to advance in the story. I bought GTA to play as a violent criminal, not a street racer... ESPECIALLY not against a driver who is suspiciously better than any other in the game. This mission would not bother me if it were a side mission, but you MUST do it to advance the game's main story. That's stupid. It feels out of place, and is not enjoyable.
I have to agree on games that grade your performance with time as a factor. STOP RUSHING ME! Isn't it good enough if I get 100% accuracy, tons of headshots, and don't get injured even once? So what if it takes me two hours to do that? If I wanted to race, I would buy a racing game.
Another thing that gets on my nerves are cutscenes that either cannot be skipped, or are skipped if you press any button or key at all. The only thing worse than having to sit through a cutscene I've seen 8 times before is missing one the first time I play through a game because I accidentally TOUCHED something.