One notable thing about the Zelda series is that everyone has their own distinct list of favorites. It may seem like everyone "disses" The Wind Waker, but there's clearly a very positive response on this thread.
The Wind Waker is actually my second least favorite Zelda game, right after Four Swords. On my first playthrough it was actually the total opposite, being my second most favorite. Second playthroughs, however, can change opinions drastically.
I actually liked the cel-shaded art style. I didn't view it as kiddy or insulting to my manliness; on the contrary, thwarting evil, slaying hordes of monsters without suffering a scratch, saving princesses, carrying impossible loads, and participating in adult pastimes such as auctions, all as a cutesy twelve-ish-year-old, made me feel more masculine if anything. (It's weird, okay?) I do feel as if the cel-shaded style made Nintendo feel they were allowed to be a little lazy with non-central characters, though. Windfall Island, a hub bustling with people, is home to some of the dang-ugliest characters in the game, especially that guy with the messed-up hair who makes his daily walks around town. It also allowed for some bland atmosphere, like how the ocean is one flat, unbroken, bright blue mass. I appreciate the expressiveness of characters such as Link and Tetra, but not all of it is worth a 10.
The music is my third favorite in the series: Skyward Sword is first and Majora's Mask (a game with ostensibly underrated music) comes second. I can't recall any dungeon music except for the theme in the final one and the Forsaken Fortress, but I have to admit that tunes like Outset Island, Windfall Island, Dragon Roost Island, and most of the boss themes were excellently done.
The whole game is worth about an 8/10 in my book, as it's essentially one giant low point to the standards of Zelda. Some Zelda games feature better dungeons than overworld design, prompting you toward the next dungeon with increasing eagerness. In some Zelda games it's the reverse. For The Wind Waker it was neither; I enjoyed exploring the various islands the first time around, but I knew what was coming the second time, especially how most islands are mandatory for completion and don't feature much in the first place. The dungeons also did not interest me terribly. They were generally just huge and took a long time to beat, and the unchanging scenery and negligible music didn't make them look very nice on the surface. Rather than presenting deep puzzles or challenging combat, it seemed mostly to rely on wandering around the huge dungeon until you found what you were looking for. Link's slow and somewhat stiff design didn't help navigation much. In The Wind Waker, I could look forward to neither the dungeons nor traversing the overworld, and since that's physically all the game is composed of, the rating is brought down.
And yes, the sailing was also a big detracting factor. Had it been streamlined or the King of Red Lions given something to make it go faster without a sail, the whole wind aspect would have been brilliant. If you miss the spot you were looking for (and lowering the crane for treasure usually must be exact), you must veeeeeery slowly turn around and wobble your boat to wherever you missed. The wind could also easily work against you, meaning you either put up with being slow as molasses or you changed the wind over and over again. I wouldn't mind the sailing too much if there wasn't so much of it in the overworld. All this means the dungeons (for me) were lackluster and the overworld was clunky and poorly designed.
To finalize my list of low points, I actually felt the story was one of the weakest in the series (please lower your torches and pitchforks, people). The story seemed to exist from plot point to plot point rather than building any solid character development or atmosphere as it went. The very beginning and very end were pretty well-handled, but everything between (save for Tetra's unveiling as Princess Zelda) seemed to have been kind of pushed in there hoping it would all fit. Rather than having personal motivations beyond saving his sister, Link's goal usually fit into the fetch quest variety with little atmosphere or development surrounding each event. Komali and Makar were interesting diversions, but not very deep as characters. Admittedly, I looked up The Wind Waker's story long before playing the game, back when I was young and stupid and had to spoil everything for myself. This enabled me to see certain plot twists coming, which has probably biased my opinion somewhat. Still, good stories are made predominantly by execution, not premise alone. The Wind Waker had one of the best premises in the series, but shallow execution. Even on my first playthrough, I couldn't help but ask my console questions when the King of Red Lions insisted I had to put the Triforce of Courage together to reenter Hyrule. Why? Why didn't it matter the first couple of times? What makes it tick?
There are a bunch of other littler arguments, but I've covered the main points. I don't want you to get the wrong idea from this. I still like The Wind Waker, and it still deserves at least an 8/10 in my opinion. But for a Zelda game, it felt almost like the video game equivalent of a fanfic. It seemed kind of unpolished. I like the game in general and understand how others can have it as their favorites, but I guess you could say The Wind Waker didn't really "do it" for me compared to the rest of the series.