For starters lemme just be real in saying that we're at least a decade away from this ever even being a possibility, and that's IF the entire next decade is utterly disastrous for Nintendo financially.
That said, I'd still like to have fun with this subject:
Mario - No one. I can't think of anyone who designs simple platformers as well anymore. The closest is probably Michael Ancel at Ubisoft.
Zelda - No one. Again, no one really designs this type of game as well as Nintendo does. Not Vigil, not Team Ico, no one, and I wouldn't want to see it thrown to some WRPG house because that isn't what Zelda is. Again, the closest in my mind is probably Platinum (Okami). Maybe Capcom since they've made Zelda games.
Star Fox - Platinum or Treasure.
F-Zero - Sega, specifically Nagoshi's team. MAYBE Criterion but that would also mean EA.
Metroid - Zenimax. I would honestly like to see Arkane take a crack at Metroid. The Metroid formula shares structural similarities to the first person RPG game style that Bethesda and Arkane specialize in, the best example being Arkane's first game Arx Fatalis. MachineGames, being made up of former Starbreeze guys, also might not be a bad fit.
Kirby - Ubisoft or Sakurai. Preferably Sakurai, but I think Kirby's low-challenge-but-still-fun game style is basically what Ubisoft's been trying to do for the last several years but done right.
Pokemon - Blizzard. I'm just really curious to see how they would balance the different types and rules of the game. I have a feeling they would end up making a really well-crafted competitive Pokemon game.
Fire Emblem - Firaxis
Advance Wars - Firaxis.
