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.