I agree with this viewpoint and it is also my fear. Actually, I would be happy with just pointer controls for games like Phoenix Wright ,Another Code, Zack & Wiki and stuff like that. Although I do want a Wii remote kind-of setup for Wii Sports. I wouldn't really need motion controls for any other game.
Motion controls is here to stay and Nintendo is pretty good at implementing it atm. on 3DS with the Zelda titles and on console with Splatoon.
I'm pretty excited that the Pro Controller seems to have IR sensors. It suggests that Nintendo is finally going for full controller parity.
No matter the game, choose a controller you own/prefer and play it.
Seems so logical and intuitive, but somehow Nintendo has neglected this simple thing for 10 years now.