>>19578316Q: When did they decide to include Greninja?
A: All of the characters to consider were on our internal roster from the beginning of development. We had a slot for a new Pokemon reserved, but did not way for X and Y. We decided to use Greninja well before X/Y came out, based on early reference drawings.
Based on this it doesn't seem to have anything to do with the movie. I'd say the reason Greninja is in Smash is because XY needed a rep and Greninja was simply the most fit.
Moreover, what would it even matter if it was Ninja Riot's Greninja. It probably has very little characterization in movie anyway, and therefor wouldn't have much to differentiate it from a standard Greninja, other than being evil.