If you have a most wanted non-Nintendo franchise you want on 3DS also, speak up!
I can't believe I forgot Metroid. I would take a remake of Super Metroid, or a sequel to Metroid Other M (speaking of which, I wish they released that on 3DS rather than on wii. It's absolutely made for 3D!) Ooh! And a new Wave Race! (I think racers will become newly appreciated on the 3DS due to the effect it brings to the sport on handhelds)
As far as non-Nintendo games go, I would love to see a new Breath of Fire game, Ogre Battle, and a port of Odama on Gamecube (weird pinball/strategy game that used an included microphone peripheral) as well as a new Burnout (or just port of Paradise, I'd be just as happy).