Until Platinum comes out, there really isn't anything you can do. However, you can play around it with the use of Palkia. If your opponent will then drop to just Mewtwo X, you're screwed over though.
What can work though is your own Mewtwo X in tandem with Uxie, if your opponent goes for the Lone Mewtwo. You use Uxie every turn to Psychic Restore, moving to Mewtwo, who then goes back to your bench for Uxie again, Psychic Restore, etc etc. This way, you cannot end up decked out and their Mewtwo can't do anything back. If they DO play another poke, it'll be easy pickings.
The only Pokemon so far that I know of that can shut down bodies is Dialga G LV.X from Platinum.