Probably either Custom Robo or F-Zero GX, two of my all time favorite games that never got proper sequels.
I'd do a remake of the Custom Robo Gamecube game but with a more open storyline, sidequests, and gameplay that resembled the DS Custom Robo, where you could battle people whenever you wanted and could buy new parts wit the money you won.
For F-Zero GX, I'd have pretty much the same except with new courses and racers and maybe a course building mode.
Also I might do another sequel for Izuna: Legend of the Unemployed Ninja. I don't know how I would do that one though.