
Skyward Sword's motion controls make the game a poor fit.

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The Legend of Zelda: Skyward Sword was originally released for the franchise’s 25th anniversary, celebrating everything Zelda, including the bosses.

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"...but it needed to be re-calibrated often, and the Switch could have it worse without a sensor bar"
The sensor bar has nothing to do with calibration. That's entirely because of the gyroscope. In fact, I believe the game doesn't even use the sensor bar at all and only uses gyroscope aiming similar to an air mouse.
I hope we get Wind Waker ported to Switch eventually...
You can already play it without the motion controllers though. Fans made it happen to PC and it works well enough. I imagine that a official HD version would do it even better. Maybe including both methods of input. So I don't see it as a problem.
"and Skyward Sword goes so far against what the original Breath of the Wild does that the two games can feel like they're from different franchises. "
That is true. But that is because Breath of the Wild is the outlier in the franchise. So while it can be argued that the difference between game structures would be smaller with games like Wind Waker or Twilight Princess. Skyward Sword still have many conventions of the original series. So the only people that could really have issues playing it more condensed and puzzle ridden world would be the new fans that only played BotW.
And for those there is BotW 2 coming out as well.
There's a base for such a great game - just ditch the motion crap and update the graphics for HD.
When all the news I see about the Switch is about getting Wii and Wii U games, the console library is a total indie nation and remaster station.