It depends on the circumstances too, I think simply by virtue of being Japanese, Nintendo would choose Sony.
But if MS were to say for example "look we're getting kinda tired of the whole game business, we'll stake you guys and you agree to take our studios under your wing and use Windows OS. Oh and here take a big fat money bag we have a bunch of these lying around." ...
OK in that case, I think Nintendo would choose Microsoft's offer.
If the deal was
- MS moves back to focus on their Steam-like PC killer. Nintendo agrees to allow some of their games on this service (so Nintendo games on PC, but only if you use MS' service ... not Steam).
- MS then exits from the phyiscal home console scene. Nintendo will make the console box and Microsoft's studios will support that box with franchises like Halo and Minecraft w/Nintendo exclusive DLC and Rare's franchises return also.
- Nintendo console and handheld will run a custom version of Windows OS.
- While MS will have advisorial role and assist in marketing and third party relations, Nintendo has the final say on all big decisions. Nintendo also controls all royalty fees from the physical console/handheld platforms. Lets be honest MS doesn't need the money from the game business, it's peanuts to them.
