I'm kind of curious if the Nintendo movies going forward will even be "Illumination" movies because I don't know if Illumination has the staff to do all the Nintendo movies that are probably coming and still do their own stuff.
I suspect the better setup will be that Universal (if they do land a deal to get the rights to other Nintendo properties) and Nintendo will set up a studio specifically for Nintendo which Chris Meledandri of Illumination will oversee with Mr. Miyamoto.
Universal also has the Dreamworks Animation division too, so they could work with Nintendo also.
Illumination has a kind of different approach to animation too ... the story team is one team, but the animation is then farmed out, this allows for their movies to be made more cheaply. So there isn't really like an "Illumination Animation + Story" combined team all in one to begin with.