I think I know why Nintendo is doing this.
They've always been hesitant to allow voice chat, because it might mean children being subjected to all sorts of foul language and inappropriate topics. By tying this functionality to phones, they are protecting very young kids from it and also ensuring that the kids that do have it are deemed mature enough by their parents to own a cell phone.
Of course, the fact that you'll need a paid subscription to access online in the future anyway somewhat disproves this theory.