I don't really see how a Nintendo-themed FPS would work well, but that's just me.
I could see a Nintendo RPG that spans several Nintendo worlds, though. Like Kingdom Hearts through the various Disney worlds and Namco x Capcom involving characters from both companies, a Nintendo RPG would be this epic trek that takes you through the Mushroom Kingdom, Hyrule, Dream Land, etc. and meeting and battling their inhabitants, with the heroes of each world eventually joining your party. And then the boss would be a Dark Matter-possessed Giga Phazon Ganon or something. Okay, maybe not. But I'm just saying I think an RPG would be a good genre to attempt mixing Nintendo worlds again in, much more so than an FPS.
(I thought that with the Metroid-esque creatures in Twilight Princess, Samus hopping planets in Corruption and Mario also hopping planets in Mario Galaxy, that it almost looks as if they would converge onto one same final "Phazon Twlight" enemy in space - which is extremely unlikely, but if ever there was a time that their games came even close, that would be now...)
There are rumours (unless someone's confirmed/denied this by now) that Link and Pikachu are in Mario Strikers Charged. Personally, I'm not sure if it's the greatest idea to shove every Nintendo character into every Mario multiplayer game. Maybe some in a few, but I don't think everything should become a big crossover fest.