I'd LOVE to see a new entry into the Vs series built from the ground up for the 3DS. I'm not sure Vs who (Nintendo would be awesome, but I'd rather see a SSB game with Capcom characters than a Vs title with Nintendo characters), but a Namco vs Capcom would be great. Not that Namco x Capcom wasn't fantastic - I REALLY enjoyed it, and I'd love an updated, translated port of it, but I don't see that happening.
A new Metroid Prime Hunters title would be cool. Up the wifi player limit to 8 (at least), keep voice chat in, keep all of the game play modes, add all of the new hunters introduced (bringing the character count to what, 12, counting Dark Samus?), and I'll buy it. I'm not big on FPS at all, but I really enjoyed the node modes in the first one.
I wouldn't doubt us seeing more Metal Gear Solid, Saints Row, Mario Kart 3DS, Paper Mario 3DS, etc. But from the list posted, definitely Super Smash Bros 3DS.