Nintendo struck gold with the DS/Wii so basically Wii U/3DS were going to have to have some kind of "hardware gimmick/novelty/hook" (depending on how you view it) no matter what.
A 3D screen and a tablet controller were simply the best things Nintendo's R&D could come up with so they went with that.
I think that's really all there is to it.
It is in a lot of ways the direction Yamauchi mandated for the company around his "retirement" though truthfully I think he was still very much managing the company's general direction until around 2005 when the Wii was being finalized.