I think that Faron should have flooded early on, with maybe a few tweaks, and the first temple should have been in lake floria. Then a new area in faron is discovered. and that serves as the forest area.
I didn't realize the game lacking a water region until very recently, when I was going over the game again, just before my boss battle. I was disappointed, because although Lake Floria was kind of like a water temple, it didn't have the puzzle elements, or the big exploration, or the need to get to the temple before you started it. It was just like, you were in the forest, then it all of a sudden turns to water. Lake Floria wasn't so much of a satisfying temple either, I would definitely say that it wasn't as good as some of the other ones.
I wasn't disappointed. Lake Floria was the water region and swimming as Link is awesome. Then there is the flood in Faron Woods by the ****** dragon that makes you find her musical notes ;p j/k that part is fun. Then the Sand Sea- such peaceful music...
My only complaint regarding the "water area" is the elevator/wedding type music. Serenade of Water and Zora's Domain are so beautiful. Lake Floria's music- not so much. Just my opinion!
The so called water region in Skyward Sword was very disappointing. The task of collecting the music notes was boring and tedious and it made the excellent controls go to waste as they were only implemented in that one area.
I really wish they had a whole region designated to water with a water dungeon similar to Water Temple, Great Bay Temple, and Lakebed Temple. The Ancient Cistern is one of my favorite dungeons in the series, I just wish they had a dungeon that was more like a water dungeon. I know most people hate dungeons like the Water Temple and Great Bay Temple, however I personally love them.