My guess is Pokemon Go predates the DeNA deal to make full blown Nintendo games on mobile.
The Niantic higher up mentioned they had been working with Mr. Iwata for 2 years ... and that was a comment from last year I believe.
I think what Pokemon Go initially was supposed to be was a way for Nintendo to gauge interest in mobile markets without actually going mobile themselves. So they would test the waters with Pokemon Go, and let the Pokemon Company/Niantic publish it.
But what happened between then and now is Nintendo decided they couldn't ignore mobile period with declining 3DS sales and terrible Wii U sales. So they pulled the trigger on the DeNA deal, but Pokemon Go was already in development so that was going to go ahead anyway.
It's likely when Pokemon Go started as a concept several years ago, Nintendo was planning to move much more slowly into mobile.







