A couple of ideas that spring to mind are Zelda II and Faxanadu. To give either a Kid Icarus (or Metroid Prime) mold would turn them into quite different games. Zelda II would become a different take on Ocarina of Time in effect. There's no reason Faxanadu couldn't see a successful implementation in 3D. Looking through a list of NES games, I would want most of the games I'd like to see updated, Zelda II, remain 2D so I don't think they really count.
One game I would love to see get this treatment is L'Empreur, a game where you play as low ranking Napoleon and then gain abilities and more options as you gain victories. You start commanding a single army and, hopefully, end commanding an empire. I have always wanted a game where you start off a junior officer commanding soldiers like Battalion Wars, rise to commanding a battlefield like Total War, and the running a province/commanding an army like Caesar II, on up to running an empire like Europa Universalis. The Wii U would offer some great options, but it will never happen much less on the Wii U.