Conker the Squirrel (God I wish he could make it with a mighty poo stage. No way is that going to happen with the game's age rating. They could tone him down but the demand sadly ain't there. At least we have Banjo and Kazooie)
Harry the Teleroboxer (it would be insane to have a Virtual Boy rep, a boxing robot, what's not to like?)
Balloon Fighter (my most wanted retro, I wish Villager's recovery didn't kill his chances)
Satebo and Parabo (the Satellaview add-on for the Super Famicom fascinates me to this day, I'd love to see these two in the game at all, be it playable, AT or even just spirit. Plus the hub world would make such a quirky stage).
Billy Hatcher (this is purely nostalgia bias)
A random insignificant Pokemon like Tentacruel or Porygon-Z (Pokemon can have as many reps as it wants. The potential for unique movesets is infinite as are the quality designs)