Personally, I would love to see a new 3D Metroid on the Wii U. I think the gamepad would be really useful for scanning, maps, etc.

However, I think the smartest track for Nintendo to take would be to put it on the Fusion (or whatever's next) as a 'core' launch title, make it gorgeous and overflowing with particle effects to really sell the new systems power. Same goes with the next 3D Mario. Practically it needs to be a launch title for their next console, perhaps with a remaster of Zelda U.

So day one people would have Mario, Metroid and a Zelda. That would move consoles.

Well Nintendo is already working on Metroid Wii U (probably will see announcement on E3), and I think they will realase F-Zero too for Wii U, and I would love to see Luigi's Mansion on Wii U, another game that skipped Wii console.

Shinya Takahashi, Nintendo:
So it has been a while since we released the last one and we're having discussions internally about what we can do next. So at this point we have two different types of Metroid games. We have the Prime style of Metroid game and we have the more traditional style of Metroid game. We feel that we do need to take care of both of these styles of play. And the hope is that at some point in the near future we'll be able to share something about them.
http://kotaku.com/nintendo-is-planning-a-future-for-both-2d-and-3d-metroi-1590142491

Mr. Miyamoto, you recently asked me to ask Kotaku's readers to say which games they'd like you to make for the Wii U. Your question was extremely popular and I got a lot of replies—more than 3,000. And a lot of them involved a particular word: Metroid.
http://kotaku.com/shigeru-miyamoto-we-have-an-answer-to-your-question-1597993025

This is why this E3 is going to be NUTS. In 2016 they will already have Mario and Zelda out of the way. We'll have a Donkey Kong, a Pikmin, a Mario Kart, a Mario Party, Smash Bros, and Star Fox, what the hell else could they possibly announce?

Particle effects in metroid would look great, and fit the atmosphere well. I think thats a great idea, but off topic question: why the hell does everyone want games to look so damn dusty nowadays? It totally fits the atmosphere for some games but in others its a hinderance, just saying.

I think a remaster would be awesome for Nintendo's next console(bet they call it 'The New Nintendo' ;P). Problem is, porting games from power PC architecture to x86 takes a bit of work, they would need to get on it asap.

Perhaps I will! >:3

Metroid for sure(imo), but who's to stay Retro isn't working on two projects? Naughty Dog did just that with Uncharted 3 and The Last of Us and correct me if I'm wrong, they're a 2nd party studio for Sony. Maybe we'll see Diddy Kong, a Tales of game, or a new Paper Mario or Luigi's Mansion. Perhaps Megaman(he was in Smash afterall) or, and this one is my personal favorite, a console Golden Sun. GOD would I love to see that.

Any way you slice it though, besides Metroid everything else would kind of be out of left field. I'm hoping Monolith was developing two projects. Xenoblade Chronicles X this year and Baten Kaitos U next. That would be amazing. 

See there's plenty of options out there for Nintendo. They've been making console games since the early 80's, they have such a big pool of IP's to draw from that hopefully old and exciting things are just around the corner :)

-Metroid - very likely

-Animal Crossing - very likely

-F-Zero - probably

-Pokkenn - probably

-Fatal Frame - probably

-Another GC remake - probably

-Luigi's Mansion - maybe

-Paper Mario - maybe

I expect some of this game at E3 this year.

Nintendo is not really larger now than they were then. inflation wise maybe, but not truly