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I have a preference for Pikachu, so that's what I voted. But, this is one of those it could go either way scenarios.
If we are talking within the limits of the main game mechanics, Mewtwo wins hands down.
Change that to a more open battle system, like the Anime or PokePark Wii's battle sequences, and Pikachu could win by swinging around, staying in Mewtwo's blind spot and spamming moves. (Just like how I beat Zekrom in PokePark 2).
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