Current Series:
Mario
I've never supported Toad, I don't think Waluigi is important enough, and Bowser Jr. isn't a particularly compelling character to me. I think the Mario series is well-represented enough; the only newcomer I actually like deserves to represent his own series.
Zelda
I love The Legend of Zelda, and I think there might be room for some reshuffling or to cut and add someone. Link, a form of Young Link, Zelda, and Ganon should all stay. As much as I'd love to see Ghirahim, Tetra, or the Skull Kid, they're each important only to one game (kinda two in Tetra's case) and therefore don't truly deserve a spot in my eyes. The only newcomer I can throw my unbiased support behind is Impa. She's been in a number of Zelda games and had a major role in the most recent (Skyward Sword). I think she'd take Sheik's slot. In terms of Zelda and Sheik, either they can split and stand alone, or they can tag-team swap with down-B instead of transforming.
Kirby
There aren't many more major Kirby characters, but following Return to Dream Land, I must say Bandana Dee would make a great addition.
Metroid
Metroid certainly deserves another rep, and there's no one better in my eyes than Samus's nemesis Ridley. Just as long as they don't use his atrocious Other M design.
DK
Following Diddy's much-awaited inclusion in Brawl, I think another DK rep is in order. I don't know whether I prefer Dixie or King K. Rool though. Dixie was partially in Brawl, so I think she's fairly likely, but I think K. Rool would be a cooler addition.
Fire Emblem
I dunno much about this series, but I must say, we need Roy back with a different moveset.
Kid Icarus
Lady Palutena gets my vote here.
Sonic
If any third-party series deserves a second rep, I think it's Sonic. My vote would have to go to Knuckles here, though Shadow is a close second (and probably likelier).
New Series:
Paper Mario
Paper Mario has the potential for a really great moveset, and seems to me like the most logical choice to represent the Mario RPGs.
Mega Man
The Blue Bomber absolutely deserves a spot in Smash Bros., be it his classic form or his X appearance. The moveset potential is astounding and he's an important part of Nintendo's history (and vice versa).
Castlevania
Alucard or a Belmont absolutely deserve a slot in Smash Bros. They have unique moveset potential and again are important to Nintendo.
Punch-Out!!
Little Mac. He SO deserves a spot, being an old but loved franchise that had a revival a few years back.
And unlikely as it is, I'd truly love to see Quote from Cave Story in Smash 4. It would never happen, but he'd fit beautifully into the game.