Ok so the 16th Pokémon movie aired in Japan a couple of days ago and I just thought of something about the new Mewtwo "form"
According to Pokébeach ad other moviegoers, the Mewtwo in the movie was cloned from Mew by different people other than the scientists who made the Mewtwo we've known and loved for 17 years. This explains why it sounds more feminine than the Mewtwo from the original movie. So basically Gamefreak is making Mewtwo a new Pokémon again by making a different Mewtwo with the new form. So maybe this is a new Pokémon like it's been advertised as and not just another new form.

Game Cannon /=/ Anime Cannon

Sorry but I just really hate the idea of there being multiple legendaries in game cannon, especially one that's as powerful as Mewtwo.

I mean seriously, what are the odds that someone would manage toclone Mew again and it'd come out exactly the same!?

The point here is that it didn't, and that's where the form comes in.

I don't like it due to my eternal loyalty to Mewtwo, but it is an interesting and plausible idea.

What if Giovanni's wife is Team Flare's boss? Lol.

Suppose you're right, though. I don't think this would change the time frame unless it REALLY had to go that far back. Say someone found Mew's luggy in the pond and sells it to Team Flare so now Team Flare is going around collecting funds to make the other Mewtwo. Other Mewtwo happens, end of story. I just feels like Team Rocket all over again.

Side note- Anime canon, who created Mewtwo? I know Team Rocket does in the Manga, I mean, c'mon... It's awesome. Just some random scientist created it in the anime?

This theory is false, Mewtwo changes form through MegaEvolution.

Yeah I know