Disclaimer: I've only played the original Gamecube version of the game and my opinions/thoughts are based on it.
The Wind Waker is my second least favorite 3D Zelda game (Skyward Sword taking the top--or should I say bottom--spot 'cause of it's excessive handholding and lack of exploration) despite it offering the best exploration environment. (which is my favorite thing in Zeldas) in my eyes.
The things that I really love in The Wind Waker:
The artstyle - I admit that when the game was released I was bit disappointed how it looked so different than OOT and MM but after I started to actually play the game, I quickly fell in love with the artstyle. I think that the artstyle is a perfect fit for the game's world and it has way more character and expression than any other Zelda game (even more than Skyward Sword).
The characters - TWW has some of the best characters of the whole series. They are expressful and have clear, enjoyable personalities (even though Tetra gets kinda downplayed later in the game..).
The exploration - I think TWW offers the most enjoyable environment to explore out of all 3D Zelda games. The world is bright, colorful and vast. The sailing music is one of my favorite Zelda themes ever. Sailing in TWW felt enjoyable and relaxing where as riding Epona (or loftwing or being in wolf form) always made me feel like I was in a hurry to get somewhere.
These are the things that I absolutely adore in TWW. Unfortunately there are couple things that really bring the game down for me:
The difficulty level - Zelda games aren't generally known for their difficulty but usually they still offer enjoyable challenge. TWW never did that to me though. The was extremely easy from start to finish. This isn't necessarily a bad thing for everyone (TWW was the only Zelda one of friends had ever managed to beat and it made the game feel that much more fun and satisfying to him) and while I'm certainly not saying that Zelda games should aim for Dark Souls level of difficulty but I still want to feel at least some level of challenge in games I play to feel satisfied by the experience.
The dungeons - I honestly can't remember much of the dungeons in the game and none of the bosses aside from Puppet Ganon + Ganondorf have stuck to my mind. TWW dungeons were really unmemorable for me and that is a bit of a letdown.
The Great Sea - I know this will sound very contradicting 'cause I love sailing in TWW but I wish that the sea itself had had a bit more to offer. I'm not even sure what exactly would have been good content to add to the sea but after exploring a square in the map I never felt any need to visit it again unless a quest demanded it. It basically turned to additional "unnecessary" piece of water that I had to travel through. Despite loving sailing it felt like a chore at times.
TL;DR: I love the feeling of the game but the actual game part of it felt lackluster and tedious compared to other 3D Zeldas to me.