You are missing something.
You don't use your Moltres/Zapdos against mewtwo, you use them against other pokemon that have less attack. Try using them against Mewtwo and they'll be as *frail* as Ray.
If Ray gets hit by FB, it can survive three more confusions. Dragonite can survive four more, a difference of just one. You should try dodging with the Dragonite aswell ;)