Let's see... who COULD be in Super Smash Bros. Clash (that's what I've been calling a fourth entry)?
From Donkey Kong, I guess Dixie Kong would be the next logical step. There could always be more playable female characters, and I could definitely see her played much differently than Donkey or Diddy by using her prehensile ponytail.
From Legend of Zelda, I would make the standard versions of Link, Zelda, and Ganondorf the "toon" versions of the characters (with Zelda being able to turn into Tetra from Wind Waker). Why? Because the "toon" versions of Link have now been used more consistently for the series than any other adaptations of the characters and are probably more recognizable as such. We can always just make Skyward Sword Link the unlockable version.
From Starfox, maybe replace Wolf with Slippy. I know people hate Slippy, but at least the frog could play differently enough from Fox or Falco. He could put more emphasis on weapons combat (I guess sort of like Diddy Kong) and jump higher than his teammates. More likely, Krystal would make it in, but I wouldn't totally count Slippy out.
From Pokemon, can we please replace Jigglypuff already? I'd recommend doing a female Pokemon Trainer, possibly to represent the newer generations. Pikachu and Pokemon Trainer (Red) have the original games covered, so maybe Hilda / White can be the female trainer using Snivy, Pignite, and Samurott. Would rather have this character replacing Jigglypuff than Lucario (would be weird to take possibly the most popular Fighting Pokemon out of a fighting game).
From Fire Emblem, I'd like to see a more magically-inclined character from the series fighting here. The only problem is that I can't really think of anybody specific off the top of my head.
From Mother, let's turn either Jeff (from Earthbound) or Duster (from Mother 3) into a playable character. The idea here is to get a character from the series who relies much less on psychic powers and more on gadgets.
I would recommend a character from Kid Icarus about now, but I haven't finished Uprising yet, and Palutena would probably be too powerful (then again, Mewtwo was supposed to be the strongest Pokemon).
Frankly, I'm wondering if they'll improve on Subspace Emissary and want to speculate on bosses for that. Two good ones I've got are Medusa from Kid Icarus and Reshiram & Zekrom from Black and White (commanded by N?).