Why is that ?? Why does this game receive not as much praise by Zelda fans when games worse than it, such as A Link Between Worlds receive so much praise. First off, before we go anywhere, that was an example A Link Between Worlds is an excellent game but I don't feel it is better than Wind Waker.
There are a few reasons that I'm going to touch on that have been brought up and addressed about the game and how I feel about them.
Reason 1
The Art Style
Reason 2
The Map
The amount of water was the biggest complaint, so much so that when Nintendo remastered Wind Waker on the Wii-U from it's original Gamecube format they shrunk the map to decrease the amount of sailing that needed to be done. When I was younger at first I thought there was so much sailing as well but then I realized it wasn't that bad and since the music was so good that it made things fun. Now looking back even further and having played it again one thing I realized is that all of those squares on that map you bring up, each and every square has something to do in it. Whether it's a fight with monsters, a tiny island to explore with a potential mini-dungeon, destroyed ships to explore, treasure to find, or in the case of the markers on that map the big islands and places to go as well.
It is a tad unwarranted to just say, "well it's just water on that map and that's so boring", because it's also a part of the story as well. All of that water is just an entirely flooded Hyrule. Underneath all that water is what used to be the Land of Hyrule which puts into perspective that all the sailing you do is not much different than all the running around you would normally doing in Hyrule, it is just water instead of land.
Reason 3
The Wrong System(s) & The Wrong Timing