Ok, do I have to bring in the trend that appears in smash games again?
Least deserving or reps: Protagonist only.
Protagonist + sidekick
Protagonist + sidekick + villain
Most deserving of reps: Protagonist + sidekick + villain + 2nd protagonist.
That's the trend, really in most cases. As the rosters expand in each smash game, there's the possibility of one or two reps added and they go in this order. First comes the protagonist, then the adding of a sidekick, then the adding of a villain, and then another sidekick.
Mario
SSBB: Mario (p) + Luigi (s)
Melee: Mario (p) + Luigi (s) + Bowser (v) + Peach (s2) + Dr. Mario (??)
Brawl: Mario (p) + Luigi (s) + Bowser (v) + Peach (s2)
Doctor Mario was just an extra anomaly for Melee.
LoZ
SSB: Link (p)
Melee: Link (p) + Young Link (s) + Ganondorf (v) + Zelda (s2)
Brawl: Link (p) + Toon Link (s) + Ganondorf (v) + Zelda (s2)
It's hard to tell whether Zelda comes first or after Young/Toon Link though.
Donkey Kong
SSB: Donkey Kong (p)
Melee: Donkey Kong (p)
Brawl: Donkey Kong (p) + Diddy Kong (s)
Kirby
SSB: Kirby (p)
Melee: Kirby (p)
Brawl: Kirby (p) + Meta Knight (s) + Dedede (v)
MK and D3 might be interchangeable in their roles. Maybe that's why Dedede wasn't included in Melee, because Sakurai thought that if he included him as a villain he'd have to include a sidekick too? (too much rep for the time?)
Star Fox
SSB: Fox (p)
Melee: Fox (p) + Falco (s)
Brawl: Fox (p) + Falco (s) + Wolf (v)
Probably the best example for the trend, because you can actually see it one by one.
Metroid
SSB: Samus (p)
Melee: Samus (p)
Brawl: Samus (p) + Zero Suit Samus (s)
ZSSamus actually counts as a sidekick character, even if Samus and herself are the same person. Ridley didn't get in despite popularity because Sakurai didn't think Metroid deserved a third villain representative.
Pokemon however, is an oddball. It seemed like Smash followed the trend from SSB to Melee (Pikachu as the protagonist, Jigglypuff and Pichu as sidekicks and Mewtwo as a villain) but in Brawl that idea went to hell. For starters, Mewtwo was scrapped and Lucario doesn't count as a villain, and Pokemon Trainer was brought in so it seems we have two protagonists and two sidekick characters. Pokemon, unlike other series, actually does depend on popularity much more because there are tons of recurring characters to choose from and the only way to single one out from the other is how popular they are.
I do think that Pokemon should have a character that can count for a villain though, whether it's Mewtwo or not, even if I miss him so.
I should make this into a thread, actually.