Well, what can Mewtwo do? Genesect resists Mewtwo's STAB attack and is SE against its psychic typing.
It's movie-wise... not game-wise.
But the producers would still have to follow the in-game mechanics to some extent. Anyways, I guess when we go with some movie logic, Genesect would get the upper hand in the beginning. Mewtwo tries its psychic attacks directly at Genesect, gets surprised that it doesn't work and then gets hit by one of its bug attacks. Mewtwo gets beat up. And then using its IQ of 10,000, he psychically searches the vicinity for a nuclear missile and telekinetically throws it to Genesect along with a Fire Blast. End of..
Genesect uses U-turn and switches with Dark Plate Arceus .