I'll always remember the "Tobybro" from generation 1 Pokemon. It was the only Pokemon that could really stand up to Mewtwo. It was a Slowbro. It has Surf, Amnesia, Thunder Wave, and Rest. The Psychic sub type and Slowbro's high Special would keep Mewtwo from pummeling it. Thunder Wave to slow down Mewtwo and hopefully cost him some turns. Surf to pummel Mewtwo once you got in some good Amnesias, and Rest to recover what damage he did do.