ALL legendaries. They're supposed to be one of a kind, that means no one should have them. The fact that their stats are high doesn't make them any better than other pokemon. Just because Arueseus hase a base stat of 720 doesn't make it invincible. It's also stupid seeing 2 or 3 Groudon or Rayquaza on the battlefield at the same time. Mew, Celebi, Jirachi, and Deoxys (all forms) are already banned, so the other legendaries should also be forbidden; There's approximately 500 pokemon now, not 30. It would be nice to see some of the 470 other pokemon in a 3D battle.
Mewtwo is one in particular that should be banned. Its very wide moveset makes it frustrating to beat. It can learn shadow ball to beat ghost pokemon, flamethrower to beat bug pokemon, and brick break to beat dark pokemon. These moves, in addition to psychic, and a base stat of 680 makes Mewtwo far too strong to be used.