Kanto and Sinnoh
From Sinnoh, I think that Dialga and Palkia would be good opponents and would give fight, but Darkrai and Arceus would beat Mewtwo without a problem.
From Kanto, Mewtwo would beat any of the 3 Birds, but Mew, as was seen in the movie, gave fight.
Johto, Hoenn and Unova, I'm not...