Hopefully the Complete Monster route. It would be neat to see a Pokemon villain. Genosect could be an Expy of Mewtwo, except pure evil.
For added awesomeness, make the movie be Mewtwo VS Gene/osect. The Zouark Movie had older legendaries with Celebi and the Beasts. So have Mewtwo be in the city where Gene/osect is made, and fight it. It would be a very interesting dynamic, as Mewtwo would see the similiarites between it and Gene/osect.
Not sure why this hasn't been Confirmed already, but yeah. There's a Genesect movie (with five of it). And Mewtwo's in it. No real word on the Complete Monster aspect though (although the manga shows four of them (Red excluded) doing a Heel–Face Turn).
Red Genesect is not a Complete Monster and does make a Heel–Face Turn too, but prior to it, it was indeed the most genuinely "evil" Pokemon the anime has had in quite a while. Even Kyurem was just kind of amoral and had a sense of honor: this thing was legit Ax-Crazy.
Here is a theory that I didn't add, as it's all discombobulated: