Well... here's a personal list of mine. I don't necessarily want every last one of these characters, just a select few. *Note: Nothing against Sonic or Snake, but I feel that 3rd party factions shouldn't have more than one character from their series... What Sakurai did with implementing Shadow as an Assist Trophy or Tails, Knuckles and Silver as background goodies is more of what I would prefer. That's just my cup of tea.
Faction
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Character - Reasoning
Super Mario Bros.
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Dr. Mario - My personal favorite from Melee... Even an alternate costume would be nice.
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Princess Rosalina - I don't know, there's something about her that I've gotten an instant liking for... She would have potential. Even an alt. costume for Peach would work for me.
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Cackletta & Fawful - A tagteam, so to speak. One goes in, the other can swap out... More Zelda/Sheik oriented, rather than Pkmn Trainer.
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King Boo - Now, here's a pipe dream. I've always been rather fond of the Boo family, and after seeing how a regular Boo fairs in Mario Party...well...I must say I was impressed with how they could work "fighting".
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Prince Peasley - An awkward choice, but hey, it represents Superstar Saga, I suppose.
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Princess Shroob - Again, another awkward choice, but adds another "female" character, and represents Partners in Time.
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Princess Daisy - Either make her playable, or keep her as that "alternate costume" for Peach. Either works.
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Paper Mario - (Like we need more Marios!) Would work similar to Game & Watch, and even be flat. Represents the Paper Mario series.
Yoshi's Island
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Kamek - Hey, I've always wanted to beat the stuffing out of that annoying magical Koopa...
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Bandit - As there aren't too many Yoshi characters...this guy was the only one I could see fitting, even if he is just another enemy in the game. He's Yoshi's rival in some minigames, so why not?
WarioWare (or, under the Wario faction)
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Waluigi - Keep him as an Assist Trophy, or make him playable... though, in my opinion, he still needs to prove himself worthy in an actual Mario/Wario title (as a villian, or otherwise).
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Ashley - Just because she seems really bad-!?
DK
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Dixie Kong - A very popular choices from the Kongs... She even appeared in her own title to save Diddy and Donkey Kong, and apparently had some data in Brawl. Who knows...
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King K. Rool - The DK series needs to have a villian representing it... Why not the infamous King K. Rool?
Legend of Zelda
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Tetra/Toon Zelda - Could help represent the Wind Waker series... and there's a good chance she wouldn't stand as a clone of the regular Zelda/Sheik combo.
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Vaati - One of the more "original" bosses in the Zelda series, and has his own little fanbase.
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Imp Midna/Twili Midna or
Wolf Link & (Imp) Midna - Personally, I just want Midna in in some shape or form as playable... She's one of the coolest Zelda characters you'll see, and very popular.
Metroid
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Ridley - Sure, he was a boss in Brawl... but there's just something different if he were playable. And don't give me that "he's too big" ploy, Bowser's huge in the Mario games (have you seen him in Sunshine, or Galaxy? Pretty much dwarfs Mario). And if Sakurai could make the pint-sized Olimar work, hey, why not...
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Dark Samus - Sure, she would seem like just a clone... but she could work out a movepool of her own, given her use of Phazon and all that. Eheh.
Kirby
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Waddle Dee, Ribbon the Fairy and Adeleine tag team - These three could work out as Pokemon Trainer does... This trio is from Kirby 64: The Crystal Shards. They haven't really appeared in any other games as main heroes (Waddle Dee's just become more of a side enemy, not a hero so to speak), and it would be cool if they were to appear to help represent the Kirby series...
Star Fox
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Krystal - A popular character from the Star Fox world... Could represent it, and also be a nice addition to the female roster. Let's just hope she has a less Landmaster-oriented Final Smash...
EarthBound/MOTHER
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Claus - Sure, he's already an "alternate costume" for Lucas, but so long as he appears as that, or even playable. Perhaps he could pull a Masked Man on us someway...
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Princess Kumatora - A nice addition, being that she could represent MOTHER 3 [help bring it to other shores] and add on to the female roster.
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Ninten - Why this guy? Just because he looks like Ness, or...? Even I'm not sure myself.
Pokemon
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Mewtwo - BRING BACK MEWTWO! Cutting Mewtwo had to have been the worst cut I've seen in any fighting game... He's a favorite with countless Pokemon fans, and is extremely powerful... Just because a majority of Smashers from Melee exclaimed his moves in Melee "stunk" doesn't mean HE was unpopular character-wise. Just remodel his moves some, and I'm sure people will be praising him as he should be.
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Darkrai - Why Darkrai? He's just a personal favorite of mine... and had a pretty cool movie to boot. He's also been rampantly appearing in other Pokemon titles as either a "major" villian, or otherwise just shown (Pokemon Ranger Batonnage as the end boss, Pokemon Mystery Dungeon 2 as causing an evil scheme you must prevent).
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Pokemon Trainer Girl - Could be the rival to Pokemon Trainer (Boy). Could possibly have Piplup, Bayleef and Blaziken? Just thoughts.
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Deoxys - Although the hype for this Pokemon has died down quite a bit since he appeared just as a Pokeball summon... I still think it would be pretty unique add, due to his shiftshaping abilities.
Fire Emblem
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Roy - BRING BACK ROY! Although Roy was just put in for promotional usage... he's become insanely popular with Smashers. It would be pretty cool to have him back, even if Ike's moreorless his replacement... But hey, if Ness and Lucas can work out together despite their similarities, why not?
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Lyndis - Though I'm not much of a Fire Emblem fan, ever since I learned about Lyn I've wanted her in as playable. There's just something about her that just screams playable, heh. She could also help boost the female roster...
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Mikaiah - Again, I don't know much of Fire Emblem... I just know that this femme fatale could help represent Fire Emblem: Radiant Dawn (and the female roster).
Other strange additions + 3rd Party
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Mega Man - Rivaling up with Sonic as another popular 3rd party choice, Capcom's Mega Man has the potential to be one of the Smash world's more unique characters, with the ability to copy defeated opponents abilites and whatnot... and perhaps bring along an Assist Trophy or two (Bass, Protoman, etc.)
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Geno - Very popular amongst Super Mario RPG fans (if you've played Super Mario RPG, he's in a lot of their parties), and was also highly wanted to be in Brawl... I'm sure the Smash team could make him work, if they could get him in some how...
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NiGHTS - Just a personal favorite of mine, heh heh.
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Wart - What's with this guy? Why hasn't Nintendo brought him back countless times to be abused in party games or crash in kart races? Is it because he was from that Doki Doki Panic game, or...? Still, I've always been fond of Wart returning some day... Why
not as a Smasher? Why
not?