Stealth Rock. I don't like Rock-types, and I really don't like the fact that this makes two of my favorite types, Fire and Flying, more useless. It's just such an irritating, overused move, and everytime I see it mentioned, I just want to sock something.
Any moves that cause Confusion, Sleep, or Paralysis as well. I absolutely loathe status effects in video games. They're just these hindering annoyances that make the game harder to play and are too inconsistent/random with their effects. I don't mind Poison/Burn though because these aren't really based on chance so much.
Low accuracy moves. Like another in this thread, I'd rather use Flamethrower than Fire Blast. I don't like the chance or the risk. Also, Focus Blast. So many Pokemon have it as the only Fighting-type move they can use and it's SO unreliable. I wish there was an alternative or that these Pokemon could use Aura Sphere instead.
And recharge moves. Like Hyper Beam, Blast Burn, etc. Especially with Hyper Beam. It was such an awesome move in the anime, one that makes you go: "Oh crap!" This overpowered beast of a move... I really would have loved to use it so much, but that recharge turn is just killer. (It's basically the equivalent of using two 75 base power moves, which sounds considerably lamer) These moves to me are a huge disappointment. I'd like to see these moves receive more utility in the future, particularly since moves are becoming more and more powerful from when Hyper Beam was first created. So I don't think it'd be too overpowered if they had it decrease your stats instead like Close Combat. Either that or just increase the base power. (to 180, perhaps. That way, it's more so like using two Flamethrowers in two turns.)