Well if there was any confusion, Iwata just cleared this up in a interview with Time Magazine:
http://time.com/3748920/nintendo-mobile-games/?xid=tcoshare
"Development of smart device games will be mainly done by Nintendo, but it is significant that we are forming a joint development structure with DeNA. Nintendo, through experience in the dedicated game system business, is good at making traditional game products. But for smart devices, in addition to the “product” aspect of a game, the aspect of an ever-evolving “service” is very important—a service that encourages consumers to play every day even for a short time. DeNA has extensive know-how in developing the “service” side of things, and will be primarily responsible for the service-oriented operations. We will be able to greatly leverage strengths of each party."
DeNA will be handling more of the service side/back end stuff, Nintendo will be leading the game development aspect, which is kind of what I suspected.
