Dragoncharystary
Smash Lord
I'm also thinking there could be another Pokemon stage for each version. Not sure what the Wii U one would be (would love something from Colosseum/Gale of Darkness), but I'd imagine in lieu of a Pokemon Stadium 3, they'd go with the Pokemon World Tournament from Black/White 2.
(Ironically Mewtwo was banned for being a "Legendary/mythical Pokemon," thus never actually was able to fight here)
As for themes, pretty sure we've gone over all of them to death and back by now. Seems inevitable that the "Kanto Legendary Encounter" remix would be in/considered "its" theme.
That would be an awesome stage. This also could happen because we have two X and Y stages so we might get something other than X and Y for a stage.
I'd love to personally hear an extended, remixed, more industrial yet upbeat version of the music they used in the first movie when Ash first meets Mewtwo (start at 2:40 if it doesn't automatically do it.) Of course, it would be better if it was part of a compilation mix with other themes. Like a more modern version of this song, maybe make it more metal and make it more upbeat.
I like the second one and remember that from the anime a couple of times. I don't recall any anime representation in Smash Bros. in the past but it still could happen.