Now for mine:
I love Persona 3, but it would've been better without the "Your friendship will get stronger soon." message. I want my friendship to get stronger NOW! Half the times you hang out with friends, you get this message instead of a social link level up. It's nearly impossible to maximize all of the social links without a strategy guide, so why not just let the friendship level up every time you hang out, instead of every other time? That way we could still spend extra days doing something different.
I love Halo Reach, but it would've been better without concussion rounds. The drop ships were much better when they just shot plasma balls at you. In multiplayer Matchmaking, the concussion rifles only seem to damage enemy players when they feel like it. There just wasn't any need for it. The Covenant already have explosive projectiles, and they're much better than that one.
I love Shadow the Hedgehog, but it would've been better if it didn't take itself so seriously. The game was clearly designed to pander to the kind of children who think that edgy stuff is cool, but they still made it tame enough for parents to approve of. So Shadow fires guns, but the human enemies don't die when you shoot them. They just lay there going "please, no!" and Shadow says "Damn! Not here!" when he falls to his death. They try to make the game look like it's dark but Shadow comes out looking like a parody of himself.
Left 4 Dead 2 without the jockeys. I understand they wanted to look different enough to justify making a whole separate game, but they didn't need to add so many special infected. And this is one of the most annoying.