Skyward Sword's motion controls are likely gone for the next installment anyway.
There's not many Nintendo IP outside of the Wii Sports ilk that are reliant on motion gaming. Mario/Zelda/DKC/Kirby/Smash/Mario Kart/Pikmin/Metroid work just fine without having to wave the controller around.
Though obviously the 3DS still has the tilt/gyro functionality anyway if you want it.
That's not good enough. And even if SS motion controls may not be continued, Wii Sports and more games like that may be designed. How will people play that on the go? It renders their experience unplayable.
Unless Nintendo offers some kind of translation of motion controls to trad controls, then maybe. But it's far-fetched. How do you translate Wii Sports controls to trad controls? It might be viable to support portable play only. Maybe in that regard it's doable.