The most menacing Pokémon of all is back. Mewtwo won't be available for 'free' for everyone, however — only for players that purchase both the 3DS and Wii versions of Smash. And he won't be available right away, either.
Mewtwo will be a DLC character players can download in Q2 2015. Apparently they're not done building him yet!
Complete speculation, but I'm guessing he won't be the only downloadable character we'll see in the future. And I gotta give props to Nintendo for giving people incentive to purchase both versions of the game too. Clever, clever.