>>32238735Rayquaza is just a wild animal.
Mewtwo, as the Pokédex entries indicate, is a fighting machine. That's what it was engineered to do and the only thing it can think of, besides conserving energy when it isn't.
When the dex says it's battle abilities were raised to the ultimate level it obviously isn't talking about the base 154 Special Attack. It means things like precision, finesse, reaction time and fast decision making, all those skills that make you a competent fighter. Because of the way Mewtwo was engineered, I believe Mewtwo's skills are perfect and the Pokédex entries are my basis for that belief.
Rayquaza may be able to match Mewtwo on terms of raw power but like I said it is just an animal. I don't think it's skills in battle go beyond firing beams and claw or tail attacks in the general direction of its targets. Mewtwo will block, dodge, aim and etc.
Mewtwo also has two different mega evolutions which makes it a lot more adaptable than Rayquaza. And in a real, unbridled battle without any plot armor I'm not sure what would stop it from just grabbing Ray with psychokinesis and asphyxiating or otherwise crushing it and blocking or dodging all of its moves with Barrier and Teleport.
