I'd love to see a Xenoblade game that was an action RPG like Nier Automata or FF16, marrying Monolith's awesome worldbuilding with a more active combat system.

Zone of the Enders is in the MGS universe

Eternal Darkness as a real time strategy game. You choose your allegiance to an Ancient, and do battle with armies of the other Ancients throughout various time points in history. Humans would be neutral initially, and can be possessed / taken over to become a part of your army.

Ratchet & Clank as a rougelite. So you start with your level 1 lancer and find different weapons and upgrades during the run.

DKC as a 3d platformer, it's about time DK made another trip to that genre.

Oh well, it doesn't play out as well as it doe in the head. 

True! Although I think Ghost was meant to be more of a stealth game, given the games name after the stealth unit. I had a more Gears of War or Warhammer 40K: Space Marine style in mind! Something more fast paced with emphasis on action heavy combat. I feel like that could work really well! 

That is actually an awesome idea! Such an under utilized game character for Nintendo.

No really diferent genres, just diferent presentation within the genre they are already a part of: 

Granblue Fantasy in a traditional RPG style. At first I thought Relink was gonna be it, but it wasnt. All scenarios were more like arenas. This IP seems perfectly tailored for an open world-esque traditional RPG were you recruit characters as you go and explore the world, villages, sky islands and whatnot.

Fire Emblem, but with units intead of individual characters. Having built up units of 5 characters ala Ogre Battle or Unicorn Overlord would make me like this franchise way much more, and then you wouldnt have to bench so many characters. 

An old issue of Nintendo Power in one of their prompts mentioned the idea of a Wario RPG and the potential of the motley crew he would bring together. That gets my vote in addition to fans getting a new Wario Land as well.
The Mother/EarthBound series has amazing potential as a 3D platformer, I think. I've long accepted we're not getting Mother 4 and shoot even a spin-off in a different genre is a very long shot.
I don't know if this is an entirely different genre but a Gridiron football game for Mario would be cool. Nintendo seems too fiscally conservative to publish such a game because outside of the United States and Canada it would struggle to sell. Do you think a sizable audience exists in Europe, Japan, and the rest of the world for Gridiron football even with Mario attached? It's doubtful. I could see Next Level Games working on it (they made the Strikers game and a cancelled Mario wrestling game), but it's still a tough sell.