How about a pokemon movie or game where mewtwo leads a revolt against humans and begins altering poke balls to catch humans and Ash realizes the only hope is to catch celebei to travel back in time and build an bitchin team to do battle with mewtwo?
I am fairly sure they wouldn’t do that for the anime or game series, for it is a little too dark and complicated. Mewtwo’s story in the anime is really well established and already has been turned good (plus Ash would never do all that work, especially in a single movie - at his very best he becomes friends with legendaries).
On the other hand, you should try reading Pokemon Adventures. I think you’ll find interesting plotlines that are a bit darker like that. I know there are some freaky mutations, and trainers actually catch legendary Pokemon in that. The battles are more intense too, and stories are much deeper. The manga tends to be darker and much more complicated than the games and anime. Here is a link to the manga.