If you could pick any third party to work with Nintendo on any game, what would it be?

Ubisoft to take the pirate and ship battling parts of Black Flag and make a game with Nintendo (with its own, non related to AC story and art style). Black Flags was just so much fun. Except the real life part.

Bungie and Nintendo to make a Metroid Prime game.

This ... 

And a AAA console JRPG with SE would be amazing ...

Rockstar and Zelda.
Bethesda and Pokemon. (A console, open world game. Or maybe a remake/sequel to Colosseum and XD!)
Valve and Spla2n.

I would like Rockstar to work on a Zelda, but I don't know about Bethesda, and Valve,

Let Nintendo make Klonoa

Fire Emblem with Creative Assembly - The Fire Emblem series has ties to the Strategy and RPG genres, but this collaboration would focus more on the strategy. Creative Assembly has a fairly solid record making turn-based/real-time hybrid Strategy games despite the problems of Rome II, and I figure that the large casts of characters in Fire Emblem could easily translate into leaders of larger armies. The scale could be a bit smaller than typical Total War game, with battles of hundreds of troops rather than thousands, instead focusing on the interactions and development of individual characters. They're already mixing things up with Warhammer, why not throw in shapeshifting dragon people?

Theatrhythm Zelda with Indies Zero - Indies Zero is the developer of the Theatrhythm games alongside Square Enix. So far, that series has tackled Final Fantasy and Dragon Quest. Thing is, Curtain Call ended up having over 220 songs from the Final Fantasy series. The only other gaming franchise that deserves a title celebrating its music is The Legend of Zelda. It couldn't be a direct copy of the existing Theatrhythm games, but this is the logical next step for Theatrhythm.

I dont think Bethesda would be able to meet Nintendos standards.

A Nintendo x Capcom Fighting game would be amazing.