Greninja was the logical choice for a Pokemon newcomer. No one changes forms anymore, so it had to be a Pokemon. Should be gen 6 as well, to promote X and Y. Who better than the Charizard of gen 6, Greninja? Pokemon is a very big franchise. They have already added another item for Pokemon, suggesting that the series might occupy a slightly larger space in the game. Brawl had six functional Pokemon characters, and with the four we have, plus Jiggs, and Mewtwo, that also adds up to six.
Also, Mewtwo will most likely be unlockable and not be revealed until after launch.