First and foremost: More Kirby characters. Meta Knight and King Dedede would be awesome. I mean, Christ, HAL makes both games.
Also important: It'd be nice to see updated version of the characters. Vacuum Luigi, a new Samus with the updated Gamecube possibilities, maybe a waterpack Mario, maybe a cel-shaded Link (instead of young Link), those additions would be nice. Maybe even new Fire Emblem characters.
I think generic enemies should stay out, including things like goombas, koopas, stalfos, space pirates, etc. Heroes and bosses only.
ThePerm, that is a wonderfully awesome idea for a stage. Wow. You should freaking mail that to Nintendo, cuz that would rock.
I thought an evil villains Smash Bros. would be cool, but releasing more villains on the regular game would work, too.
Captain Olimar using Pikmin is a definite character. Be hard to think of moves, but it has promise.
Edit: Oh, Shadow Mario could be cool, too. Maybe, combining another person's idea, have a transform between Baby Bowser and Shadow Mario, like Shiek/Zelda.