Metroid x Megaman, I can see the two doing fairly well in a Castlevania Portrait of Ruin type game, basically just take the Megaman styled level design, throw hidden items in there, and link them together with a sort of overworld deal with the more puzzle Metroid segments.
I'd buy the game a million times.
A Zelda by From is what I've wanted ever since playing the Souls game, I feel like that would actually work really well. Dark Souls already has some bits that are a bit puzzle-ish, and if you give it a sort of baseline "what you might have", it'd work pretty damn well. Basically replace Lord Souls with trinkets. I'd love that.
I wanna see companies cross games into the Nintendoland framework, personally. Seeing franchises like Megaman, Bomberman, Harvest Moon, Ristar, Gunstar Heroes... a whole variety of focused, polished titles, brought together under an umbrella, released with some love and care.
Nintendo vs Capcom developed by the TvC team
Nintendo Wars x Valkyria Chronicles
Fire Emblem Musou EDIT: Fuck it, Nintendo Musou
Mario X Sonic (platformer)
Kingdom Hearts-esque Nintendo x Square - Nomura-esque convoluted story.
Hunter S. Thompson
Edgar Allen Poe