Hrm...
Lucas, Claus and Ninten (from Mother) as alternate color schemes for Ness. (When in the Lucas or Claus color scheme, his hat would be gone.) (aside from Claus in the form you see him most of the game, Lucas, Ness and Ninten are really interchangable in terms of fighting styles. Seriously.)
Eve from Mother would be a neat Assist Trophy...
Kumatora would be a greater fighter, so would Flint (both from Mother 3)
And, for a fantastic boss sequence, Heavily Armored Pokey crashing around the stage in his spider-like mech, firing weaponry...
A Mr.Saturn 'tower' Assist Trophy would be great, as would Salsa and Yokuba...
Saturn Valley would be a great stage, as would Fourside (different design and layout than Melee's) that would occasionally switch into a neon Moonside...