Okay, you're idea is fairly good, but there's one problem. Mewtwo is a modern Pokémon that didn't come around until the modern age of the PokéWorld (yea, I know this is an alternate plane of existance and all, but still). Perhaps if you made a back-story about HOW Mewtwo got to the ancient world of the past, it would make the story a bit better. Just a thought.