I feel Nintendo will try to avoid that happening. The new Mario Party is one of the few exceptions that I've seen to this, and you can still play it in table top mode at least. I can't imagine them allowing that for a game that's 20+ hours long.
I wouldn't be shocked if the game is heavily retooled for the Switch to make use of regular controls.
I love Skyward Sword, it's right behind BotW as my favorite of the 3D Zeldas. But of course there are improvements they could make, tone down Fi, for one, and that would make a huge difference.
I imagine they would make an alternate control method for handheld use, the dual sticks will help in this regard. I love the motion controls in this game, though, so I'd play with split joy-cons as much as possible.
I'd love to see what Nintendo would do with the conversion to HD. I doubt they simply port it, they'll probably upgrade textures and touch the painterly effect in some way and maybe add some other effects as well.