^
Mario: Fire Flower, Racoon, Doctor Mario, Clasic outfit, Frog, Bee, Penguin are all viable, with the last three being kind of an eyesore and thus unlikely.
Luigi: Again Fire Flower and Racoon, Mr. L.
Mewtwo's armor should Mewtwo return, also all Pokemon should have their shiny variations.
Ike has his Hero, Ranger and Lord classes at the very least.
Snake has a wide variance, MGS1, Tuxedo, Old Snake, Plisken, Big Boss camo (since he's an amalgam of Solid and Boss anyways) of course, I'd love to see a
liquid outfit, because Liquid is a legit clone.
Ganon could've had his old Guerodo garb, or his Wind Waker outfit, or a Phantom Ganon mask.
Yoshi should've had a Boshi outfit.
Samus should have her various power/slim suits.
etc.,
Part of me disagrees with character "invasion" I think that if a character is similar enough, they might as well be an alt costume to an existing one. For examle:
Sonic should have had all of his furry friends as alt costumes, since the movesets would pretty much have been the same.
Pokemon Trainer's alts should've been similar Pokemon that could've learned the used moves (IE; Charizard's moveset exhibited lined up really well with Aerodactyl and, save for fly, Tyranitar/Nidoking, and Squirtle's with Mudkip. Pikachu fits well over Raichu)
I'd like to see a clothing option similar to the stickers, really. It'd be a lot of fun. And of course, there's two ways to make it chooseable: Your name, or with the usual X/Y button type deal.
Perhaps we'll get something like this for the customizable portion of the game on the 3DS.