This is my modest 45 character dream-roster, trying not to cut any characters I think are significant.
[COLLAPSE="SMACKAKOW"]
F-Zero: 2
Captain Falcon
Black Shadow (Give Ganon a new moveset, leave me a character that hits like the boston molasses disaster, also I've wanted to Falcon Punch this guy for a while now)
Donkey Kong: 3
Donkey Kong
Diddy Kong
King K. Rool
Super Mario: 6
Mario
Luigi
Peach
Bowser
Paper Mario (Deserves it)
Geno (Unlikely, but I think the Mario RPG's are deserving of 2 reps and who better than Geno?)
Warioware: 1
Wario (Do we really need more?)
Ice Climbers: 1
The Ice Climbers
Yoshi: 1
Yoshi
The Legend of Zelda: 6
Link
Zelda/Shiek
Ganondorf
Toon Link (New moveset, slightly)
Vaati (Why not make it 2 for the toons, he's also the second most prominent Zelda villain)
Midna (I'd rather have Skull Kid but I'm not sure what he'd do)
Star Fox: 3
Fox
Falco
Wolf
Fire Emblem: 3
Marth
Lyn (Marth + Captain Falcon? :D)
Ike
Pokemon: 5
Pikachu
Mewtwo
Jigglypuff
Pokemon Trainer
Silver (Totodile, Bayleef, Typhlosion)
(The only Gen V pokemon I'd want is Scrafty)
Pikmin: 1
Olimar
Metroid: 2
Samus
Ridley (Bowser's been huge before too, no reason you can't downsize)
Sonic the Hedgehog: 1
Sonic
Metal Gear Solid: 1
Snake
Megaman: 1
Megaman
Mother: 2
Lucas
Claus (Arm Cannon, sword, lightning, bat wings, pretty much one of the coolest characters you can ask for)
Kirby: 3
Kirby
Metaknight
King DeDeDe
Kid Icarus: 1
Pit
No More Heroes: 1
Travis Touchdown (Would just be funny)
Golden Sun: 1
Isaac[/COLLAPSE]
Also, does anyone else think that Final Smashes could be much better implemented through some sort of SMASH METER that builds up over time, much like other fighting games?