This is to show off the new Mega Evolution, obviously. Mainly sort an advertisement of the changes introduced.
Also, it can be assumed that this takes place in an alternate universe on the whole. Funny, I know, but it explains how his age never changes.
Also, this has happened before, where Ash meets a Legendary once, but it is kind of forgotten, in a way. I guess that is to help with the story line. So as to the exact reason, should be better answered by the Pokemon Company, but this is what I feel.
All the originality is not lost though, as
>In the credits, a reference to the original Mewtwo is made when the Mewtwo in this film is shown standing on top of a building overlooking a large city at night. This is the same scene that the original Mewtwo last appeared in at the end of Mewtwo Returns.