I don't get what all the "Mewtwo's no longer possible!" business is about. Charizard and Greninja did not take away from that. What happened was that since mid-match transformations no longer exist, Red is no longer applicable.
Charizard merely got his own slot like ZSS and Sheik, and Greninja only replaced Squirtle--no one else. This only tells us that Meganium, Sceptile, Torterra, or Serperior will be replacing Ivysaur. Either that or no leaf starter at all which is doubtful now that we've seen Greninja, but hey if that DID make a spot for Mewtwo I'd be all for it.