Well since Kalos is almost over I might as well say what I wish to happen. Mewtwo from the first movie should come back and train with Ash. Not travel on a journey but whenever Ash has to fight someone like Tobias in a future Pokémon league Mewtwo will want to test its strength against these strong Pokémon. I also believe that it should evolve into Mega Mewtwo X to showcase the Mega Evolution. I know that many of you will say Mewtwo is too proud of an intelligent Pokémon to want to associate himself with Ash, however like I said, the reasoning could be that he wishes to test his strength. I know the writers don't like doing things like this because it's fanservice, but hey! One can dream right?!!
Another reason it could train with him is because he believe the strong bond in Mega Evolution between trainer and Pokémon is the only way to increase his strength.
I seriously doubt Mewtwo would appear or train with Ash. With the Kalos league currently being held and with only several episodes left of the Kalos region, I don't think Mewtwo has any reason apart from X mega evolution to appear in the series. Ash is certainly not going to train Mewtwo in my opinion.