It's more Mewtwo looks like Freiza, but to be more exact, Freiza's head upside down creates Mewtwo's crotch.
Actually, the guys who invented Pokemon said in an interview a few years ago that Mewtwo was inspired by Frieza. They wanted someone completely evil and strong and with DBZ being such a hit, they took inspiration from the person who destroyed a planet by lifting his finger.
I know right. I still can't get over how Freiza destroyed 5 minutes in 5 weeks with Namek- wait, FFFFFFF-