Using the article I linked above, this could give us a few assumptions.
1: Snake
Kojima said he was not aware if Snake was in the game. This statement was after development started. Since I would assume Kojima would need to be asked for permission, that means Snake will not being returning. Or at least I would say that if Kojima wasn't a massive troll. I don't see snake returing, but it's not impossible.
2: Mewtwo
At last year's E3, during the pokemon X & Y roundtable, a fan asked if Mewtwo would be in Smash 4. Sakurai responded from the audience, "We are thinking about it." Seeing how smash started development in March 2012 following KI:U, Sakurai at that time had already known for a year if Mewtwo was included or not. I doubt he would speak up like that if he was aware the answer would be no.
3: Lucas
Just elaborating on Sal's leak, I quote “All of the characters you see here and pretty much all of the characters that we’re still looking at have… were all decided right at the very beginning of development." This means while the roster was decided, they are still polishing some characters. This means Lucas just may be the one they chose to cut mid-development so they can dedicate more time to debugging, seeing as the release is inching closer and closer.
Any other characters you think could be effected by this?