I have to say Wind Waker is definitely my least favorite. I never played the sequels, but I can assume they're just as bad. (especially, considering what was said about them.) Wind Waker, to me, was an utter disappointment and I don't even consider it a part of the Zelda franchise.
I wasn't partial to the graphics - they just felt cheap, and frankly it seemed like the design team didn't even try and put effort into them. They were just slapped on, and the game was sent about on it's merry way. There was no detail, and I'm a stickler for detail, so that was a big thing to me. Cell shading is good for anime, and that's about it. I couldn't take those graphics seriously and it hindered me delving myself into the story and plot.
The story line was lacking, and took much too long to come together. It just seemed like they were drawing it out, for the sake of drawing it out and having a longer game to sell. Even when it did start to build, it just wasn't that interesting to me. I will say this - the only interesting thing about the story line was the fact that it hinted at being a direct sequel to Ocarina of Time's story line; the fact that Hyrule was dragged under water after a hero was sent back in time, etc.
Plus, once the story line started building, the game play became much too tedious.
I mean really... first we go through all those temples... then we have to collect a bunch of maps, only so we can turn around and collect that many more triforce pieces. Quite frankly, hunting for that stuff in all that ocean was nothing short of aggravating.
Which, brings me to my final point. TOO MUCH OCEAN. There was waaay too much ocean, and that boat didn't nearly go fast enough. Relying on the wind was a pain - if you had no wind, you didn't move. I would play a boating game if I wanted the feel of really sailing. Plus, as Shadsie mentioned, scrambling to get back in the boat while under attack was a major annoyance. You shouldn't have to stop, every time you become encumbered by enemies. Epona doesn't stop on land, so why should the boat stop. (especially with so much ocean to escape to.)
Wind Waker was just... ugh. So much could have been done, and yet so little was given.