Assist Trophies:
Marx, from Kirby Super Star: when activated, he picks a random spot on the screen and does the "split apart then form black hole" attack. It would suck characters in and deal damage, then hit them upwards, like the Starfox bombs.
Rawk Hawk, from Paper Mario: The Thousand Year Door: his attack would be a hearty yell of "IT'S TIME TO RAAAAWWWWWWK!" followed by a series of body slams.
If they plan to make another detailed story mode like The Subspace Emissary, then I think Bleck from Super Paper Mario should make an appearance. I don't know how, just work him into the plot dammit!
Characters:
Krystal, from Starfox: her attacks could incorporate her staff and the powers it has in Starfox Adventures to make her less of a semi-clone of the existing Starfox characters. Her Final Smash could be an airstrike that works kind of like Snake's grenade launcher. Anything would be better than another goddamned Landmaster.
(Maybe they could change Falco's Final Smash into an Arwing shooting gallery for a limited time? Personally, he prefers the air, after all.)
Leon Kennedy, Resident Evil 4: I'm not familiar with Resident Evil, so I'll just say his attacks could involve a plethora of guns, roundhouse kicks and knives. His Final Smash? Um, maybe a close-range grab that leads into a rocket to the face?