We see "new IP" all the time in the form of fresh skins over copycat games - like the army of military themed first person shooters. People seem easily tricked by a coat of paint.
Nintendo is talented at creating characters and worlds because they put a lot of care and crafting into them. This makes them conservative about creating "new IP" as people perceive it, willy-nilly. They seem like they don't want to waste shots at new properties by tossing out something unoriginal and half-baked.
They do need to create new characters and worlds, because they're very good at it. But never mistake that for not making new "gameplay", which Nintendo does all the time. If anything, they are entirely predicated on making new ideas and gameplay.
Not only Atlus for Fire Emblem, but also Namco for Smash Bros.
Considering Nintendo struggles with third parties, and time requested for HD development, I think that this could be an interesting way of pushing more games on the market for the Wii U.
Of couse, those should be smart partnership, especially in terms of genre (not as an action for Metroid)
That said, I honestly don't know which other partnerships I would like to see.
Mario and Sonic in a crossover title where they each take on levels from the other's games that have been remastered. Mario in Sonic game stages and vice versa complete with powerups remastered from those games to work for the new protagonists. Its just gimmicky enough to sell me a copy.
Fantasy Zone x Star Fox
Cave X Nintendo would make me excited too but it'll never happen. I'd like a dedicated Nintendo bullethell and crossover cast starring in it would thrill me.
I haven't really got anything special though to add. I just woke up.