Well, Twilight Princess is a better looking, better controlled, better written, and better made version of the 'Zelda formula' and a better game all-around than Ocarina of Time.

Whereas Skyward Sword's controls never worked for me, was WAY too hand-holdy, and just didn't work, story wise. Skyward Sword is in my 'terrible games in otherwise great franchises' list, making it my single most despised Zelda title by a pretty wide margin.

I genuinely don't know how people like Skyward Sword.

Well, speaking as someone who did have some issues with it but still really liked it overall, it was the satisfying motion-plus-powered swordplay and brilliant dungeon design that made it most enjoyable for me.

Really? I played it for like 24 hours and I could never get the swordplay to work. I was constantly having to recalibrate every 5-10 minutes, and even the simplest puzzles just didn't work for me. An early puzzle had you trying to disorient three eyes at once, and no matter what I did it just didn't work. I guessed the solution and tried it, but it didn't work. I googled said solution to see if it was the right solution (it was), and it still didn't work. I then watched a Youtube playthrough where they showed the solution (Same thing I was doing) and it worked for them but not for me. I wasted somewhere between 30-60 minutes JUST trying to get that one puzzle to work. 

As for the dungeon design and such, I found it was WAY too much handholding. I don't mind some handholding (Wind Waker and Twilight Princess both had a lot of it), but this was far, FAr too much. To me, this Zelda game was like...what if Portal gave you the solution to each puzzle room then told you to do it? Not just 'speedy thing goes in, speedy thing comes out" where it explained physics and let you figure out the solution. To me this was more "Speedy thing goes in, speedy thing comes out; So, if you are falling quickly and put a portal here and here, your momentum will continue and you'll get launched into the air in that direction, whch is where you want/need to be. Now, go ahead, do the puzzle! there's a 95% chance of this working for you." 

Oh, and Fi. Probably the single worst character in any videogame ever. Navi was bad enough, Fi was worse. As a joke, not funny. As an assistant, not helpful. as a personality, blank. IT was a nothing character that just pissed me off any time they were on screen. 

I actually LIKE the idea of a linear zelda, I just don't think this game pulled it off. Furthermore, I like the idea of a character driven Zelda story, but I don't think this pulled it off, either. I don't hate those elements, I just don't think they add to the game while the handholding, terrible controls (in my experience) and boring design really ruined it for me. 

IT's been a long time, though. Maybe I should give it another chance. I haven't played it since 2013 or something.  

Control wise I dunno what to tell ya, that simply wasn't my experience. And while she/it was kinda meh, I didn't find Fi that big an issue either.

Sections like carrying around the Time Crystals, rearranging the rooms of the final dungeon, or the heaven/underworld duality of Ancient Cistern were just genius in their design and among the most inspired levels in the series and genre for me.

I didn't get that far. I think I made it somewhere between the fire temple and the next temple...which is NOT 24 hours to most people, but like I said, every puzzle required an excessive amount of time to make work and I kept dying to simple enemies becuase the controls just weren't working for me.

Twilight Princess. I played through it twice on each platform it was on (GC, Wii, WiiU) and never even finished Skyward Sword. SS just felt like work to me instead of a place I could escape to. I just wish I could relive my first play through of TP.

Once again, I genuinely don't know what to tell ya, the controls simply didn't give me that kind of trouble. Maybe your Motion Plus was busted?

I thought that, but I used two separate Motion+ enabled controllers (the black ones where the + was built into them), and a white one with the attachment. Same issue every time. 

At E3 2010's stage show didn't the controls in Skyward Sword go haywire when they tried to show it off due to IR interference from the audience's phones?

Midna