This is the thing I don't get. Most all of 3d Zelda's zones are like this. The Southern Swamp in MM for example needs you to
-Lily pad skip over poison water
-Keep up with a monkey through a forest maze
-Backtracking for Red potion
-Taking a boat ride across the swap
-Stealthing through a Deku court yard to speak to the king
Almost each of these major gameplay elements take place in their own rooms. All the rooms are fat hallways with one in and one out. Success in each of the elements serves as the key to the next area. And with most of the area landlocked by the poison water your actions are pretty directed though the were typical Zelda goodies hidden in its corners. The whole Deku Stealth segment is about as gamey as you get. I just don't see where the huge disconnect is.
I think the disconnect is simply that Skyward Sword (and Twilight Princess, and Phantom Hourglass and Spirit Tracks, I think) attributes relatively less meaning to any of your actions. The lock-and-key mechanism feels more transparent in those worlds, whereas Majora's Mask tries to create an organic presentation that facilitates layered meaning.
When performing actions in Majora's Mask, someone is always affected - you see and feel an aspect of a character or a situation that builds on the game's core themes (e.g., loss, death, fear, maturity, worship, etc.). Skyward Sword, at multiple junctures, skimps on such opportunities: in places with obvious potential for character or scenario development, the game simply skips off to the next locale, eager to cast the player into more entertaining, but somehow disconnected experiences.
Consequently, when Majora's Mask ends, the relatively simple plot has been overshadowed by layers of complexity, giving the impression of weight, of substance, of accomplishing more than merely fitting all the right keys into the right locks. When Skyward Sword ends (and this is at least my feeling after 60 hours), all that remains is the relatively simple plot, with a few flashes of character development that either do not integrate well with each other (main characters and side characters), do not utilize their full potential (
), or do not really synergize with the gameplay (Fi).
That's my feeling on the matter, anyway.
And in line with the current discussion: I enjoyed all of the dungeons, but the music in the Water Temple has never grown on me. My fiancee, who also loves Majora's Mask, can barely stand it. It is kind of grating.