A common gameplay trait in some of the more recent games has been to have a 1st Half of the game (several dungeons), then a major event/turning point, then the 2nd Half of the game (several more dungeons).
Examples of this include OoT (gather spiritual stones, get MS and wait 7 yrs, awaken sages), WW (gather pearls, get MS and find Hyrule, restore MS power and gather triforce), and TP (gather light spirits, get MS, gather mirror shards).
I'm hoping that they DO NOT use Skyloft/Hyrule in this way....meaning, I hope that the first half of the game IS NOT in Skyloft where you defeat a couple of dungeon, followed by changing the Skyward Sword into the MS, and then going down to Hyrule for the 2nd Half of the game and defeating a few more dungeons.
I hope they come up with something much more clever and interesting than that for this game. That outline has been a bit overplayed at this point.