Wow, I had to register as soon as I saw this, because I have a lot to say... here we go...
The first thing that comes to mind right now, thanks to recent time spent playing Killzone: Liberation, is boss fights which are an order of magnitude more difficult than every other part of the game. I can go through the rest of that game on the highest difficulty level, but when the boss fights come, I'm hard-pressed to beat them even on the easiest. If the rest of the game was so masochistic in difficulty, it would be expected, and acceptable in my eyes, but done like this, it's ridiculous. Mechassault 2 is another good example, especially since I don't think it's as good on the whole. The difficulty curve makes things challenging but managable for the whole game, until the last level, which may as well cause a foot to pop out of your Xbox and kick you in the balls.
Bioshock has been mentioned, so I must now bring up vita-chambers, or any other game mechanic which makes it more or less impossible to genuinely fail. You could just load whenever you die, but I shouldn't have to take an action like that in order to artificially increase the difficulty level to something less than laughable. I can say wit a fair amount of confidence that I have had bowel movements more challenging than Bioshock (bad dietary decisions...) I like games which I can actually lose. In fact, even in multi-player I get bored with a game quickly if I find I almost never lose. The adrenaline just doesn't flow when that happens.
In contrast to what some people have mentioned, memories of Far Cry Instincts prompt me to bring up levels in which enemies DO see friendly NPCs, and proceed to slaughter them mercilessly, leading to failure. I gave up on Doyle and just used the level unlocking cheat on that one, since the part of the game in question was at the end of a level.
How about jumping puzzles when you can't see your feet? I'm looking at you, Valve. If the Source engine can't pull off showing me my feet, you need to come out with a new version of it, or stop doing jumping puzzles, because they're just frustrating.
Another thing that bugs me are 'sandbox' games which are only non-linear when you aren't doing a quest. Bethesda harped about freedom in Oblivion, but this usually comes down to 'Yes, I'll help' or 'Maybe later.' I shudder to think that these people are making Fallout 3, because they haven't demonstrated that they can make a quest worthy of Fallout. Hell, even Fallout Tactics gave you a few different options on how to accomplish a clearly defined and non-negotiable objective. In Fallout and Fallout 2, many quests could end in different ways, or at least play out in different ways. I realize Fallout games are not sandbox, but the quests in them are often less restrictive than those in supposed 'sandbox' games.
While we're talking about Oblivion, how about NPCs I can attack but can't kill? If I stab or shoot someone, it should hurt them. Doesn't HL2 kinda do this as well? Would it be that hard to simply make it so that the player character will not use their weapon if it's aimed at a friend? This would also solve the problem on children in violent games, or at lease lessen the problem.
Hm, more on Oblivion... level scaling. They said, in Oblivion, it would mean things would remain challenging, but given the simplistic combat and easily exploited magic system in the game, it really just means they never are. It also breaks immersion, of course. I liked in Morrowind how I could get my ass kicked easily if I was not ready for an opponent, but if I came back later I'd mop the floor with them. Being able to sneak past or outsmart enemies for a fantastic reward is also good.
Also present in the astoundingly disappointing train wreck that is Oblivion, are NPCs to whom you can say multiple things, each of which gets an identical or nearly identical response. Patrick Stewart was apparently delighted to voice the emperor, I don't think it would have been hard to get a few more lines out of him.
Forced stealth missions. I was very relieved to find Rainbow Six Vegas didn't have one, like most of its predecessors. I understand the reasoning behind them in the R6 games ("If you knock people out, the bad guys will get suspicious and may find the bug you planted"), but most games don't have solid reason for this annoyance.
NPC soldiers who you are supposedly leading but can't actually give orders to. The idiotic marines in Halo 3, who struck me as significantly more retarded than those in Halo 2, remind me of this. When did HL2, a wildly successful game, come out? 2004? In HL2 you can tell your NPC buddies where to go, at least. They aren't especially bright, themselves, but you can make up for this by making decisions on their behalf. Bungie could have learned from this. Maybe it is a deviation from the feel of the first two games, but it would not have been a drastic one if done well.
Games that use the same aiming system for grenades as for guns, requiring an unrealistic and irritating amount of guesswork for their effective use. This is not believable or fun. I was baffled when Splinter Cell: Double Agent did away with the wonderful grenade throwing system of its predcessor, Chaos Theory. This is a common problem, and the reason I almost never use grenades in any shooter (the 'sticky' grenades in Halo are an exception due to their unique nature).
The so-called 'no-scope'. Most rifles built for sniping lack any built-in aiming devices. Why should people still get a reticule when using something like that without the scope? I like the TF2 way of doing this.
I have to agree with the 'Simon' crap, although it did give me a good laugh while haging around a Gamestop. An attempt at playing the Heavenly Sword demo ended abruptly because I was *gasp* actually trying to pay attention to what my button pressing was causing to happen in the game, and I apparently hit the wrong button. God forbid people should want to focus on the character they're controlling instead of big ugly pictures of gamepad buttons. What's the point of making the cool sort of scenes this stuff usually accompanies if people are forced to focus on the 'Simon' game?
Oh, there's more, too, but I want to get my thoughts organized before continuing.