...you knew I'd come here, didn't you you little worm?!
A few Calm Minds and recovers would make M2 invincible to any special attacks from Rayquaza. One Ice Beam would OHKO Ray easily. Ray is too weak. Not even crunch against Mewtwo could kill him. Face it, you little maggot, Mewtwo is better than Rayquaza.
Here are the base stats:
HP
Mewtwo: 106
Ray: 105
Attack
Mewtwo: 110
Ray: 150
Defense
Both: 90
Sp. Attack
Mewtwo: 154
Ray: 150
Sp. Defense
Both: 90
Speed
Mewtwo: 130
Ray: 90!
I told you. Ray doesn't have a faster speed. He also has lower Sp. attack than Mewtwo. I WIN! YOU LOSE! MEWTWO WILL DOMINATE RAY! With a few Calm Minds, Mewtwo Sp. Attack and Sp. Defense will far surpass Ray's. Even with Dark moves on ray, they'd be USELESS! Ice Beam from a Cm'd Mewtwo would KILL RAY IN ONE HIT!
Stats taken from www.serebii.net