The Wind Waker was an awesome game. However there are some things that could have been executed better.
The number one complaint among fans and critics seems to be exploration, which revolved around sailing the Great Sea. I personally thought sailing was a great aspect of The Wind Waker, and is what set it apart in the series. My only problem with this aspect was the lack of interesting locales to explore. It would have been nice to visit an island inhabited by pirates or a small port town that featured an assortment of minigames. It would have also been cool to explore Great Fish Island post-destruction. Moreover, seeing a few other travelers on the sea would have been an interesting addition. That way, the player would not have always felt so alone out there (I know, there was the King, but still...). Some other interesting things could have sprung from such an addition as well, such as more side-quests and seafaring 'missions'. That brings me to the 'Search for the 8 Triforce Shards' quest. It felt as though it was forced in at the very last minute; it was arguably the most tedious part of the game. It could have been better executed into the story. Adding mini-dungeons hidden on a few of the smaller islands would have likely resolved that issue, as well as given many of the barren islands an actual purpose. One of my fondest memories was embarking on a second quest hoping that the Koroks' efforts would be finally realized... *sigh*
Conversely....
In retrospect, I don't think the Great Sea as a whole was ever meant to be the way I mentioned above. If I recall, the latter part of WW's plot was significantly centered around the post-diluvian Hyrule. Personally, the desolateness of the sea gave me a sense of longing for the Hyrule of ages' past (of Ocarina of Time). The emptiness and lack of settlement on its various islands was very effective in that regard, as it left me [the player] emotionally connected to the story. Simply put, if the Great Sea was 'perfect' and brimming with activity, the player [and characters] would likely be content with the way it was, which would have detracted from that emotional aspect. The plot of the game would also have been different, as Link and Tetra would have not needed to search for new land - a new Hyrule.