I think the major idea behind an original character is that, if it's well done and TIES all these 'All-Stars' together, then it would more than likely work out.
Like Geno, basically. SMRPG was supposed to be just that, a "Mario" RPG. They could have made him and Mallow koopas or goombas, or replaced them with any of the already central characters from the Mario-verse. But with so many outside elements in the game (it was made by Square, after all,) they decided to use original characters that fit with the atmosphere of the game, tieing the new elements to the old. In a crazy game about characters from several different universes coming together, who's to say that if Sakurai comes up with a comprehensive story he won't also come up with a character that somehow unifies all these characters under one purposeful banner?
I know we all have our own characters that we're pretty vehement about leaving a slot open for, but in the end we have to remember:
1) It's Sakurai's game.
2) If he makes it work, and makes it cool, then why not. And I believe he's more than capable of making it work.