I'm a big Zelda fan, to the point where I'm always playing through the various games multiple times. I love just about everything there is to the series, soak up all the lore, nerd out over the timeline and the various implications therein, etc.. I'm a fanboy. I'm way biased in favor of anything with the name 'Zelda', and I'll not apologize for it.
The first time through Skyward Sword, I enjoyed it. Loved it, even. It was a fun romp. But the second time through? I dunno... I actually got mostly through the game again, but I didn't finish it. I got bored. Which is particularly damning in my eyes, because that's never happened before with a Zelda game. Its charm was limited, where the other games are just plain timeless.
The problem, I think, in a nutshell: it's one of the most sparse Zeldas, yet it insists on being the longest Zelda. Too much of the game is filler, and run-here-run-there quests that only serve to make you run over the same ground again. Hell, it's the only game in the franchise to make you return to a dungeon. And for sidetracky, not-actually-related-to-the-plot-or-any-kind-of-progression reasons too. It didn't bother me too bad the first time around, because I was hyped up to "see what's next!" and that gave me the energy to slog through it all. But now that I know what's coming up next -- that it's 45 minutes of running around the desert before I see anything cool -- it really takes the wind out of my sails. Collecting music notes in a flooded version of the forest you've already revisted a time-or-two is a chore rather than a cool moment to look forward to.
Granted, every Zelda game has its moments of tedium. But they don't take as long as they do in Skyward, nor are they as plentiful. Even the infamous Triforce quest in Wind Waker doesn't take much time at all if you've planned for it. You can't plan for anything in Skyward. It's going to take just as long every time, because everything is so rigidly designed to fill for time, and so linear you can't really mix it up (except for one part later on where it graciously lets you revisit the game's three zones in whatever order you please. Hoorah).
Okay, I'm getting kinda ranty and I don't think that's helpful. Here's the thing: I still like Skyward Sword. The few bosses that were in the game were cool. The characters were cool. The game's aesthetics were great. It has a lot of great moments, and some cool story implications for the series. But there's too much uneventful tedium between it all. It could have been a really awesome shorter game -- really tight with great momentum. But instead, it's a long game with huge pauses. It suffers greatly at the part where it's supposed to be game that's fun to play.
I consider it the worst Zelda. Now, I love every game in the series, so that's not such a bad insult. But yeah. They can do better.