Welp, all we need now is for one Japanese guy to get his hands on the game. Once we see the full All-Star mode, we will know what is included in the base game.
The fact that they were able to include Link into Mario Kart 8 as DLC gives me a lot of faith in Nintendo's DLC capabilities, though, if Mewtwo isn't in the game. He'd definitely be a prime candidate for an extra character later on. I hope we don't have to resort to that, though. I really hope we don't. That's a dark path to walk. There is no real hope to be had there, only blind faith.
What I mean is, while it would make sense to make DLC for Smash 4, there is no guarantee that it will ever happen, and certainly no guarantee that Mewtwo will be a part of it. There was no indication that it absolutely was going to happen for Mario Kart 8, nor which characters it was going to be. There was a confirmation of the ability - the possibility that it could happen through data diving, but no hints as to what it could be, if it would be, etc.
I guess very soon we shall see. But @
woopyfrood
is right: we have assumed that locked All-Star correlates with the roster we have seen, but there is actually no proof that they correlate. Only hope. So, we shall see.