My theory is that Mewtwo is another clone but a female version, based on the fact that it has a female voice and in the flash back we saw a differnt science crew.
Ash might not remeber mewtwo becouse he ereased his memory but if you noticed that team rocket did recognized mewtwo, I don't remember if in the first movie Mewtwo ereased their memories either.
Also the new season of Pokemon they have the MEGA stage, and this mewtwo is X...
these are the facts that makes me believe that there is going to be a sequal movie where both of the mewtwo are going to meet and this mewtow will teach the original one to MEGA evolve and we will discover how the Mewtwo Mega-Evolution Y looks like.
thats my theory, sorry for bad english, its not my native language!