Well in my opinion I believe that Rayquaza would win. Not because of the obvious reasons you stated, but because Mewtwo's strength is all derived from Special Attack but his Speed is average. Rayquaza has high Attack and Speed, making his moves almost always come first. This also allows him to use a broader range of moves that would be "Strong" where Mewtwo could only use Psychic moves. Also take into consideration that statistically speaking Dragon is the best type in it's many strengths and very few weaknesses. It only has 2 types that can strongly effect it. So in the end I agree with you.