It should be noted that Mewtwo has assets in Brawl's files, including voice acting that did not appear in Melee, presumably for a final smash. Sakurai did not intend to cut him.
As for Greninja, if Lucario, a character made popular by promotion and movie appearances, can have staying power, then Greninja, a character made popular by genuine fan adoration, has nothing to worry about. Squirtle and Ivysaur aren't nearly as significant or popular as Charizard, and their exclu ission is a consequence of the removal of transformation characters.