I think when Nintendo negotiated their original deals with the stamper bros. it was important for both of them that Rare retained their creative independence. Nintendo wanted to keep a level of financial and directorial sway. Therefore a 51/49 split was a good association. Of course this means the stampers were free to do what they wanted (within reason), including selling up their controlling stock. When MS owned more than half, there certainly was a conflict of interest amongst the two owners, so Nintendo sold up (as was probably a requirement).