Story didn't seem any more intrusive or insubstantial than other Zeldas to me. The unskippable dialogue was definitely a drawback, but it didn't kill the game for me.

I never wondered what I was accomplishing or questioned character motivation either; Link was trying to find/rescue his friend, and along the way forge the master sword, Zelda and Impa were trying to prevent the Demon King's return.

The gameplay was more a priority for me, and that's where Skyward Sword really delivered.

In difficulty I'd say it's: MM>SS>OoT>>>>>>>>>>>WW>>TP

Two things:
a. The stamina meter was great
b. The tutorial in SS was surprisingly short. Upon replaying the game, I got to the first dungeon in about thirty minutes.

Just so you know, you're conflating terms here. The story is intrusive, the plot is insubstantial (just a pet peeve of mine). Regarding the intrusive parts, I took a few minutes here to watch a walkthrough of Faron Woods (first time) and reaquaint myself with the game. During the 20 minutes or so spent there, there were around 10 unskippable and unavoidable dialogues or cutscenes, which I find pretty intrusive. Regarding the insubstanial part, compare the first act (the first three dungeons, basically) of SS with OoT. There's not a huge difference in time devoted to story, but one gets a lot more accomplished during that time.

You may not have had any questions, but I came up with a few. For instance, why was Link being forced to follow behind Zelda rather than accompany her? Why does Ghirahim not kill Link at the Temple of Time? Why is the Song of the Hero broken up into pieces? And what does Link accomplish during the first round of dungeons other than waste his time?

Ocarina of Time may have been revolutionary for its time, establishing the current formula of Zelda 3D games, but there's no denying that today, and compared to its successors, Ocarina of Time fails miserably, the other3D Zelda games are improvements over this one, even the somewhat boring Skyward Sword.

Story's not just a matter of getting stuff done though. SS Zelda made its story a lot more appealing than OoT for me, cos I actually gave a damn about her.

Link follows Zelda cos he's trying to save her but doesn't realize that she's fine on her own, or rather with Shiekah, because he's not ready yet to be the Hero of Time. Ghirahim doesn't kill Link because he enjoys toying with his prey, he's arrogant to a fault. In the early dungeons, Link is building his skill, and learning that he's not ready yet, but working towards being so. Can't remember the song of Heroes thing, last played it in 2011.

Nostalgia is a horrible mistress isn't it?

or maybe people think it's a legitimately well designed game, also for some reason the nostalgia argument applies to OoT but not to Wind Waker or Majora's Mask, I bet a lot of people here have nostalgia for the Gamecube era.

Clearly that's crazy talk. Everybody knows old games are always awful and cannot possibly be liked more than new games.

I can understand being invested in the Zelda character in this game. That said, it's imprtant to remember how much presence she has in the story. Outside of the tutorial, the ending, and a single 10-minute cutscene, she has exactly 4 lines and maybe 3 minutes on-screen. Like I said before, her parts, the best parts, are just a few moments. And the reason these moments probably stick out so prominently is because the rest of the story is so inconsequential and forgettable.

As far as the role of story, a story is exactly a matter of getting stuff done. Establishing and developing characters and setting and advancing the plot are what a story is supposed to do. If your story isn't doing those things, it's just wasting your time. OoT does those things; Skyward Sword, less so.

-It's implied through dialogue that Link was supposed to escort Zelda. Except she went off without him, so he was forced to play catch-up. Except when he does catch-up, he's told to back off. Basically, he's just being jerked around for no good reason.

-Ghirahim toying with Link made sense the first time. Maybe the second time, at a stretch. The third time, after Link stops being a nuisance and actively interferes with his plans, Ghirahim claims he's not going to make the same mistake again, and then does just that.

-"Buidling his skill" strikes me as a cop-out. The same could be said for spending 5 hours grinding in an RPG, and it has just as much impact on the story. During that time, Link unlocks the other areas of the map, which is so inconsequential it can be removed entirely with no effect on the plot.

-The Song of the Hero is the last round of questing required before the endgame. You have to seek out 4 dragons to get the pieces of the Song given to them by Hylia. Except it's all pointless because Hylia, either through Zelda or her servant Impa, could have just given Link the song instead. It's just a contrived excuse to pad out the game.