Oh sh1t thats hard. Lemme break it down just know no category will be an ez call.
Music ss, combat tp, dungeons and bosses tp, story ss, visuals ss, overworld/traversal tp, music gimmick tp, ss-3 tp-4. I guess tp wins. But barely.

When it comes to the controls I had a problem where I needed to get my sensor bar replaced. Something about the sensor bar was causing my character to walk in a circle even when I did nothing. It was happening in a bunch of games, but it was worst in Skyward Sword. Once I got a new sensor bar the problem went away.

I had a lamp fairly close to TV, when it was on, Wiimote was going haywire...but when it was off, I didn't notice any more problems with SS than with any other Wii game. Sure, it would be better if Wiimotes were at least as good as PS Move, but controls were quite adequate nevertheless.

I never had major problems with the motion controls besides the ocasional recalibration (that was as easy and simple as to press down on the D-Pad). I've heard of many people complaining about how the sword didn't swing as they wanted to. Then you see them play... and they do it like if this was Twilight Princess on the Wii: just moving their wrist quickly. I mean, you CAN make it work like that if you get the right feeling (speedrunners of this game play like this)... but the idea is to use the Wiimote as an actual sword using wider movements with your arm. If you use quick and smal moves with your wrist, the game will most likely not register them properly.

I had major problems with motion controls in Skyward Sword, which impacted my enjoyment.
First: the controls were a little too precise or complex to be fun - while precision and complexity sound amazing on paper, in practice, simplicity tended to make for a more fun and satisfying experience... except with aiming! But when I'm fighting, I just want to get in there and throw fists!
Maybe given time and practice with the interface, it would have become fun, but there was the second issue I had (read below).

Second, I always had issues with the controls being thrown off balance and needing to re-calibrate way too frequently to ignore. This made the game a little frustrating to even get used to playing.

But was that annoyance worse than my annoyances with Twilight Princess? I can't say they were.

But I'm a poor one to talk about 3D Zelda. Until Breath of the Wild, I hadn't been a fan of 3D Zelda games since the N64 era. And now, since Breath of the Wild, I can't even say that I am currently a fan of any older 3D Zelda games - though Link to the Past is still a blast to me, despite being incredibly short (5-6 hours, maybe? When playing the game, it often feels like I am just getting started and then I'm 3 dungeons into the Dark World in like 2-3 hours.

Then you're speedrunning. A Link to the Past is not that short. For a regular run to a regular person it'd be 15-20 hours.

Yeah I think that might be a big part of the problem; a lot of folks may have approached Skyward Sword as if it were Twilight Princess or a lot of other Wii games and thought a simple flick of the wrist would suffice. If you try to "waggle" (God I hate that term) your way through SS you're in for a bad time.

I like both games a lot but I prefer Skyward Sword, it has better characters, story, side quests (TP barely has any, especially NPC-related ones), combat (sorry, I didn't have problems with the controls in SS) and the dungeons have more creative and less obvious puzzles. SS also feels  more challenging, TP is mostly a cake walk. Oh, and I prefer SS's art-style and orchestrated OST.

U know what? After sleeping on it, ive changed my mind. Even though tp edges ss out by the numbers here, ss gave me the most epic feeling to the end of a zelda to date. The army battle followed by demise standing in the storm waiting for me followed by the start of the whole story. My gut says skyward sword. Also it says I need nachos.

While the controls for swordplay were better in SS, TP had the better aiming controls thanks to IR; I always thought it was a kinda weird mistake that SS only used the gyro for aiming and forewent IR entirely.