Mario: Geno and/or Bowser Jr.
Zelda: Midna, and the new and improved Young Link in cel-shaded awsomeness FORM!
Donkey Kong: K. Rool, but that is VERY DOUBTFUL!
Metroid: Ridley, or Sakurai sucks.
Star Fox: Krystal. I bet your wife on it.
Fire Emblem: Marth, maybe Roy/a new rep.
F-Zero: Just Captain Falcon, since Sakurai clearly doesn't give a care about F-Zero or Samurai Goroh.
Pokémon: Lucario
Mother won't get repped unless in the slim chance well...Ness returns. Claus is a no-chance as a PC, other then alternate colors probably, or at least IMO.
And that's it IMO, unless I forgot a major franchise, lol! XD