Well, I won't disagree with the whole disconnected fields thing... I felt that was a poor choice and that the developers didn't know what they wanted to be the overworld of the game- so they stuck with the sky because it was more different. If the other areas had been interconnected, however, the sky would have been severely underplayed- even more than it already was.
I feel that having one town was a risky choice, but I think it was to emphasize how early in the story this game is- it allowed things to be simple and streamlined. I do think that the enemy populous could have been a little higher, but I think that's because I just got used to the combat really quickly- I just really enjoyed how each enemy encounter was its own challenge and had to be faced down in a thinking, adapting manner. That's one thing that I really hate about the series in general- that the combat isn't engaging at all, and by Twilight Princess, I was more or less done with the "wait for an attack and strike" formula the series had boiled down to. The masterful sword combat in Skyward Sword is one of the main reasons I love the game.
I can't really agree with your "formal and structured" argument because that's kind of what the series is at its core, however, I think Skyward Sword suffered heavily from the development time put into the motion controls because it lacked a lot of the varied gameplay we got with Twilight Princess- escort missions and more interesting little side diversions. However, Twilight Princess seemed empty and I'd say it had just about the same amount of enemies throughout its "enemy populated areas", and the engagements were less interesting, to boot. Skyward Sword utilized its environments, which were just about the best seen in any 3d Zelda game, over and over again and in different ways that were engaging and gave purpose as to why you revisited the area. And call me crazy, but I enjoyed Skyward Sword's guardian segments because they gave purpose to the basic abilities you had and were challenging in a different way. Now, I'm not saying I liked PH or ST's guardian segments, but I thought Skyward Sword did it great.
I just think that overall, you need to take each game with the mindset that it's always going to be different. One could argue that Twilight Princess and Ocarina of Time are very similar, but I would disagree because they both have very different focuses. I don't think a Zelda game has to be land-based, classic style to be good, because they've proven that to me with Wind Waker, Phantom Hourglass, and Skyward Sword. I think a varied locale and design to the game is what keeps the series fresh. However, a larger, more populated overworld would be nice, but I'd also very much enjoy platforming and puzzling elements to be woven into the game to a point that dungeons gradually become overworld and vice versa, and you know that you're getting close to a dungeon when the puzzling and platforming elements start to become more difficult, but it's still a gradual change.
But now, Zelda to me should always have motion controls because that was the most engaging combat I've ever had in a Zelda game, and the series deserves to have a well-rounded amount of elements contributing to it, not just puzzling.