I have a feeling this is pretty simliar to how Sony got an exclusive Spider-Man game.
Basically how that came about was that Marvel approach Sony on making a Marvel game for the PS4, Sony agreed and ask Insomniac to make it for them and Marvel and Sony let Insomniac picked the character they game would of based on.
Would not be shock if it turns that Marvel asked Nintendo to make a Marvel and Nintendo agree and got Team Ninja with Team Ninja being the one's that decided it would be a new Ultimate Alliance.