Besides popularity I would like if every series had 4 characters, which allows those IP matches. Match with Mario, Luigi, Bowser and Peach on some Mario stage is epic. Because Wario and Yoshi are strongly releated to Mario I count these 2 as alternatives for Luigi/Bowser/Peach, so I don't think Wario or Yoshi need companions. Though I would like to see Waluigi allowing Mario&Luigi vs Wario&Waluigi match. Toad could be cool as a way to have Super Mario Bros 2 battle, but the others from Bowser Jr, Paper Mario and so on aren't as good, you can use multiple Bowsers and think they're different because some Bowsers look alike (especially SMB1).
So I agree DK could add Dixie and K. Rool, which would make a match of 4.
I'm not particularly fond of Krystal, but she could be the 4th Star Fox character. Although I'd prefer Slippy Toad.
Metroid really only has Ridley, unless we start to add Other M characters. I wouldn't mind if Anthony Higgs got it, first black character ever. Zero Suit can't really be counted either so I would propose another rival bounty hunter such as Rundas or Ghor.
Zelda has 4 but Toon versions don't count IMO. Though because of the limited slots to add I would accept keeping the current ones. I would like to see Ghirahim though (Tingle is just too weird)
Kirby already has 3 so they could add 4th. I don't have much preference.
Pokemon already has 4, though I would like to see more equal categorizing. Pikachu/Jigglypuff/Lucario/Pokemon Trainer is very unequal and goofy looking match. I wish there were 4 low-levels (Pikachu-Jigglypuff-Meowth and ?), 4 high-levels (Mewtwo-Lucario-? and ?) and add atleast 2nd "Pokemon Trainer" who uses 3 pokemon (I'd like Team Rocket). On the other hand I don't want Pokemon getting too many slots, so a compromise is needed.
Fire Emblem is already close to 4, although it's not quite as big series. It could grow at 4.
The other series are smaller mostly with 1-2 characters at this point, struggling to get bigger. But even they can be categorized.
So going with all star logic I hope the roster would be:
Mario Match:
Mario, Luigi, Peach, Bowser (Yoshi, Wario, Waluigi, Toad)
Donkey Kong Match:
Donkey Kong, Diddy Kong, Dixie Kong, King K. Rool
Star Fox Match:
Fox, Falco, Krystal, Wolf
Metroid Match:
Samus, Anthony Higgs, Rundas, Ridley
Legend of Zelda Match:
Link, Zelda, Ganondorf, Ghirahim
Kirby Match
Kirby, Ribbon, Meta Knight, King Dedede
Pokemon Match:
Pikachu, Jigglypuff, Meowth, Pokemon Trainer (Mewtwo, Team Rocket)
Fire Emblem Match:
Marth, Roy, Ike, Black Knight
Snes Match:
Captain Falcon, Samurai Goroh, Ness, Lucas (Little Mac, King Hippo)
Retro Match:
Ice Climbers, Duck Hunt Dog, Mr. Game&Watch, R.O.B
3rd Party Nintendo:
Simon Belmont, Megaman, Ryu Hayabusa, Pacman (Sonic, Bomberman)
Misc. Match:
Olimar, Pit, Palutena, Isaac