It probably will eventually, even if just in a special, or movie.
Yeah, I think the same thing as well. I'm hoping we have a special where the two Mewtwos meet, question each other's existence, and finally figure out how Newtwo was created with the ability to automatically Mega Evolve. Part of me likes to think that Newtwo is actually a reincarnated Ambertwo from the Mewtwo's Birth prologue, just to give Mewtwo a happy ending with an old friend of his....
Actually, that might make an interesting plot point, and it could easily explain there being Mega Mewtwos without having a trainer. Their bond with each other is enough to trigger their respective Mega Evolutions!