Pal, in this Generation of the anime, all rules are being broken, so we can't be sure about ANYTHING. If Ash's Greninja returns, he might be actually be capable of fight and defeat Mewtwo. Besides, to travel with Ash and avoid attract attention, Mewtwo can remain in a PokeBall, but that doesn't mean his Psychic powers won't work in it. I mean, in Muk's case, its stinky smell traspassed the PokeBall. And Ash won't use Mewtwo for any "unworthy" battle. In case there's another crisis like the Darkest Day, Mewtwo will definitely be handy.Sorry, but there's zero way that any Mewtwo is going to be captured at all. It's too much of an artificially intelligent Pokemon to be crammed in a pokeball all the time. What's Ash going to do? Send it out, have a conversation with it and then return it to its ball after the battle, where it'll happily remain until the next battle?
No, this isn't a Squirtle we're talking about. It won't happen.. and ESPECIALLY not with this one.
By the way, I have another suspiction. I know Pikachu, Lucario and Cinderace won't be able to defeat Mewtwo; but through this battle, maybe Mewtwo could learn to use the power of Aura by watching Lucario. After all, Mewtwo is one of the Pokemon capable of learning Aura Sphere. And if Mewtwo learns how to use that power, he might be able to bond even more with Ash.