In a way Motion controls have always been optional in Twilight Princess. The game was designed around traditional controls and people always had the option to play it on the gamecube for that. The motion controls were sort of shoehorned in to push motion controls on the Wii but that wasn't the original design philosophy of the game.
That's why it's really easy to make them optional.

Skyward Sword is completely diffrent in that regard. The game was completely designed around the motion controls and would not work without them. They would have to redesign the whole game to make it work without motion controls, which would be more akin to taking them out entirely, not making them optional. It also would require a full-on remake instead of the remasters we have been getting so far.

There would be nothing stopping nintendo  implenting the circular sword motion to the the analogue sticks in future. Just turn the analogue stick 360 degress clockwise or anti clockwise, many games that feature have QTE's started doing this many years ago. The biggest example of this mechanic is in Heavy rain and beyond two souls which constantly made the player move the analogue sticks in a circular motion.

Other than time and resources. I think you underestimate how much interface code must be rewritten to make that work. The Dolphin revisions in the examples I posted emulate motion plus on the gamepads without rewriting code. That is the best they can do. And that is just one example of a problem people face when using gamepads. There are others. It isn't just circular motion. It was a specific type of motion that suited the design of the world, otherwise just waving the Wiimote Plus in a circle would've solved the puzzles involving eyes (which it did not, you had to be in the right spatial location and do the right motion for each scenario.)  Heavy Rain was a static quick time event game not built around an interactable world. It is entirely time dependent and not spatially dependent. These are entirely different scenarios. There is no QTE engine in Skyward Sword, and they would have to adhoc one to make it work in that scenario. 

Again, while it might not sound a lot to fix just this one thing, it is much more work than you might think, and they would have to fix more than just this one thing to make it work on the gamepad. Considering motion controls were part of the major appeal of Skyward Sword, it just won't happen. I think Nintendo's controllers from now on will have gyroscopes in them. That is how Skyward Sword emulation will be done, by mapping the accelerometer and gyroscope in WiiMotion plus to that in whatever controller they have next. And it would take a lot of work to get sword play to work right with the analog sticks even then, but it is much more doable than with a controller that doesn't have any gyroscope/accelerometer at all. 

Why do you keep referencing the gamepad! There is no chance of skyward sword ever being released on wii u. Skyward sword HD will likely be coming out for the NX.

Gamepad =/= Wii U gamepad. I am talking about the common phrase used for generic controllers - "gamepad." 

What a google search of "gamepad" gives. 

https://www.google.com/search?site=&source=hp&q=gamepad&oq=gamepad&gs_l=hp.3..35i39l2j0i67l5j0j0i67j0.164.763.0.852.8.6.0.0.0.0.219.219.2-1.1.0....0...1c.1.64.hp..7.1.219.0.Gs6Ooqay_ig

And what wikipedia gives. 

https://en.wikipedia.org/wiki/Gamepad

"A gamepad (also called joypad), is a type of game controller held in two hands, where the fingers (especially thumbs) are used to provide input."

I'm still a huge fan of Skyward Sword, but I will admit motion controls did get annoying at times. And even though some cool items came to be because of motion controls, I don't think it's the way of the future for Zelda. So yes, I'm happy they are optional. And I think they should have motion controls as an option for Zelda U as well, because motion controls are a good concept, and they can add to the experience. I guess I'm in the middle on whether or not I enjoy motion controls in Zelda.

Lets all move forward...

Well i call it a control pad or standard controller, it's just a misunderstanding i guess. At least you admit skyward sword could be playable without motion controls albeit with a lot of time and effort.