Yeah I saw that the matter manip needs to be touch based, consisering flight, teleportation, and barriers Mewtwo just won't let that happen. He seems to like when he has his range.
Radiation, transmutation, and absorption seem the best for Doom, but the potency of radiation only took out a city's grid? And absorption only absorbs incomming energy blasts and missles? Unless transmutation has range or the other two are more potent than the profile implies, Mewtwo probably blocks, teleports, and generally plays keep-away and haxes super quickly for a pretty decisive win.