Exactly... except it could happen.
Maybe Nintendo realizes that some people like 3D mario and others prefer 2D mario, for example. This would let them sell a game to both. They're not just spending more to develop, they are increasing the potential sales base. And I bet developing a 2D mobile version of a game is fairly cost-effective compared to a scaled-down port of a full 3D game.
Example of a game for NX that's already kind of like this:
https://youtu.be/Ndi_46bKZVQ
Playing on the 'base' connected to the TV would trigger the 'console' version in my guess, since it will likely have more processing power.