Ganondorf and Falco are the only two I hope return (unless you count Luigi, in which case him too). Ganondorf should have a half-magic, half-swordsmanship based move set, as those are what he chiefly uses throughout the Zelda series. Falco can just be given different weapons from Fox - like others have said, bazooka, sniper rifle, a heavy blaster rifle, perhaps some mini-bombs or space-style grenades, take your pick. He'll probably get a little heavier in the process, but that'll just serve to differentiate him more from Fox.
Roy will probably be dropped for other FE characters, although I wouldn't mind if he returned personally - as with the others, he'd be easy enough to declone with different sword strokes and more use of the Sword of Seals' fire magic in his special moves. The other three I really hope don't return, since all were horribly redundant. Theres just no need for two versions of the same character, no matter whether they're just in a different outfit (Doc) or a completely different age (Y Link, Pichu).
Zevox