Like so many others, I think Simon Belmont is pretty much the best choice for another third party character. Classic NES era, iconic weapons and moves, and a tons of potential for bad-ass music and stages.
As for Nintendo characters, N from Pokemon Black and White is the best character they've had in a long time, and they could do another Pokemon Trainer thing by giving him Reshiram and Zekrom to switch out, considering those two (Zekrom especially) seem to be the favorites of Gen V.
If they're going to give the Zelda games more representation, then at least put in Skull Kid. He's the only Zelda villain other than Ganondorf really worth anything. They'll probably use Girhahim if anything, but I think Skull Kid would just be way cooler. Moon Crash for a final smash anyone?
Waluigi is the worst character Nintendo has ever conceived, but the internet has kind of elevated him into a god of ironic hipster love, so if nothing else he'd be hysterical.
I'm gonna go a little more obscure and say they should use Rawk Hawk from Paper Mario: The Thousand Year Door. He's one of the funniest characters from that game and his macho wrestling style is just begging to be utilized. Plus, the RPGs reallly need some representation.
Now, for the two that should happen, but are pretty much guaranteed to not.
It's a crime that King K. Rool has never made it in once, but considering he's not even the main bad guy of his own series anymore it'll probably not happen unless he shows up in Tropical Freeze as the surprise bad guy.
Finally, Goku should be in it. Just because I'm a huge fanboy. Hell, I'd buy the game if Snake, Yoshi, and Goku were the only three characters.