This is assuming there are no characters added by the WiiU release and stuff, I suppose.
In that case:
Lip. Oh god yes. While I am opening up to Dr. Mario back now(Big franchise, clone of the face of Nintendo, easy stuff), he is not enough to represent puzzle games. One clone is just not enough. Neither is Yoshi and the Pokes, they represent their own franchises, not the puzzle spin-offs. Which is why Lip would be perfect. She's the only character that has puzzle game origins and not alterations of other franchises. It's also a Japanese-only game, and such games are just as much a part of Nintendo history IMO. And also:she's a female, and a very young one at that. Would be a great pick.
Ray 01:While I am rooting for the GC version, I wouldn't mind the other Rays. Anyhoo, Custom Robo has been around since N64 and has a fairly good part in Nintendo history. Sakurai's old excuse about "no-projectile-main characters" has been blown to dust by Mega Man and Mii Gunner, so there's not too much of a excuse for him. Noise(The company making the series) certainly dosen't mind pushing him for Smash back in Melee for a mere Trophy, so why object to character promotion?
Issac. I'm not a big time fan of Golden Sun, but I've played enough to notice the fun, and I definately know the history of this game. There aren't that many franchises with a million seller, that has not been repped yet in Smash through playables. And there are none, no franchises that originated in GBA that has been repped. In that case, why not start with the franchise that is one of the most famous franchises that's portable exclusive.(Well DS hasn't been repped yet either, but they do have a Tomodachi stage, so...)And for people thinking he'd be similiar to Robin, I'm pretty sure that they're different.
Lucas & Wolf.Both veterans. Both in Brawl, so easy to import. Both from a under-repped franchises. So why the hell not?
Mewtwo:While I don't care much for him, I sincerely hope he's in just to shut people up. Lucario is NOT why Mewtwo was replaced in Brawl, Sonic and time constraints were. And if he is similiar enough, just give him a new neutral B.
DK rep:Either of the popular two will do. DK has proven itself to be a big franchise, so I wouldn't mind one, if not two(though that would mean that one is likely to be a semi-clone) and it would help to turn away hate saying about too much representation for other franchises(FE, Mario...)
