For the sake of Movie 16 turning out good, I hope this is Mewtwo.
If it turned out to be a seperate Pokemon, we're going to get a terrible Movie that has too many Pokemon to focus on. Movie 15 is a prime example and it felt too messy and clunky in the short period of time.
As of right now, the general plot of Movie 16 will go nicely as followed:
-Ash arrives at area, Genesect all attack.
-Mewtwo arrives to save everyone.
-Mewtwo fights Genesect.
-Mewtwo loses/severely weakened.
-Mewtwo awakens new forme and stops all the Genesect.
If we have another co-star (MewXY) then either Mewtwo or MewXY will lack screentime or some form of glory, and if it happens to be Mewtwo then people will rage that his return was wasted (including me).