A recent Japanese livestream of Pokken Tournament showed off a secret fight with a dark and energy-laden Mega Mewtwo. Exact details as to how to trigger this fight are not known, nor is it known if this character will at any point be playable; however, he looks like a pretty strong character with good combos and great ranged attacks, making for an exciting fight.
Unfortunately, that pretty much sums up all we know about him at the moment, but hopefully more will come to light soon, or at least when the game launches in the west when Spring rolls around.