It depends on Mewtwo's moveset. If he knows Fire Blast (which is a must on any competitive team), he OHKOs the Genesect due to him being choiced, his insane Special Attack and Genesect's X4 weakness to Fire.
What would actually happen aside, I just hope Mewtwo goes and kicks some butt instead of having his butt handed to him because of the New Pokemon Hype. I mean, just look at Gary's Electivire. That thing kicked Ash's butt. Why? Because they want to hype the new Pokemon.
All in all, the only reason I want to see this movie is Mewtwo.
inb4 Mewtwo and Genesect befriend each other at the end and defend the city together.