People don't like Wind Waker because they "judge it by it's cover". They looked at the cartoony graphics and thought "This is a kiddy game". I personally love the game. The story is amazing, the gameplay is great, and the graphics are fantastic, in my opinion. It also has the Great Sea, which people say is empty, but I think it does exploration right. This game is nearly flawless, in my opinion.
I think Wind Waker has a solid story. You don't start your quest to go after items to get the Master Sword or some other item like other Zelda games. You start your quest for personally reasons; Link's sister was kidnapped. People might not have liked that because Link actually has a character and people don't like when things are different.
The gameplay is basic 3d Zelda gameplay, but it feels better with the Gamecube controller. That's just my opinion though because I love the Gamecube controller.
I love the graphics in this game. I actually want another cel shaded Zelda game. I don't get why people hate it. My mom says that "everything is wrong" which doesn't make sense to me. The colors are amazing. They are bright when they need to be and dark when they need to be. People bash it because it's "childish", but I just think it's unique. I also like to point out that I think I remember hearing that people demanded a realistic Zelda and then bashed Twilight Princess' graphics. There's just no winning.
People also bash it because of the Great Sea. I agree, it's kind of empty, but I actually liked exploring it. If it was smaller then the exploration wouldn't be there because everything would be easier to find. It feels more adventurous to me.