Can't believe I never commented on this, but yes I found it extremely disappointing. You can point at my article and say, "Hey, you said you thought SS was the best Zelda game!" Yeah, well, I lied... Just kidding, it's actually just that through retrospect, my opinion has changed.
I found the story good, but not as good as some of the other games. My main gripe about the story, though, is that they introduce the main boss within the last 10 minutes of the game (I know he had a presence throughout the entire thing, but we learn most of what we know about him while he was in his "human form," the last 10 minutes!). On top of that, I was like, "Wait, this guy right here, who you just shoved in my face a few minutes ago, is suppose to explain the reasons behind the actions of the entire Zelda series?! GAH!
Also, yes, dungeons were short and not very challenging. Heck, Spirit Tracks had more elaborately designed dungeons! And the hamper on exploration = sad face. I enjoyed Twilight Princess hyrule field an infinite amount more than the clouds, three regions, and Skyloft. I think I'd even prefer the Great Sea over it...
Credit where credit is due, the controls were great and graphics were amazing. However, I just no longer find this title up to par with the rest of the Zelda series.