Nintendo's next home console and handheld will be separate, based on what they've been saying. They may share similar branding, but they'll be two different devices. You can't buy a console game and put it inside the handheld and expect it to work.
I don't know how much clearer this quote can get:
What will really happen is that the assets for Mario, Link, etc wouldn't have to be created twice to make a Smash Bros. for both the console and handheld. You wouldn't have to recreate assets to make both Super Mario 3D Land 2 and Super Mario Galaxy 3. You can simply use a lower resolution, lower fidelity asset for Mario for the handheld Smash, and a more higher resolution asset for Mario for the console Smash.
Create it once. Reuse it across platforms.
They probably realized their mistakes when they had to recreate assets for Mario Kart 8, Super Smash Bros. for Wii U, Super Mario 3D World, when they already existed in Mario Kart 7, Super Smash Bros. for 3DS, Super Mario 3D Land.