Different poll. This is your LEAST favorite here. Now I'm curious to see which one gets the most hate. Because that is another interesting thing about these three games to me is almost everyone dislikes one of them. Not that picking your least favorite necessarily means you dislike it, but again... curious.
Probably the Wind Waker. The ocean was vast and beautiful, and it felt truly adventureous traversing it at first, but I was disappointed by the amount of empty space compared to the more traditional fields, and having to adjust the wind direction was kind of annoying in the long run. The dungeons and bosses were a bit on the easy side, and there was too much recycled music in the game overall, for me. Some of it made sense as references to places from other games, but even in some of those cases the arrangements weren't all that creative, I thought.
I still like the game a whole lot, though. The art style was plenty awesome to me, the marine themes were cool, the new compositions were pretty, the general gameplay fantastic as usual, and the ending is one of my favourite Zelda endings of all time.
Twilight Princess, I guess. Though I still enjoyed it more than OoT, which is my least favorite Zelda. Started it at least a dozen times and quit every single one of them. At least Twilight Princess I only started once before quitting forever.
Interestingly it always seems to be the blasted Goron/mountain dungeon (whatever the game) that makes me want to stop playing... Hmm...
Wind Waker. It's just not a good game. It's all eye candy with very little substance. It was a game with a clear design focus that it was going to be as easy and accessible for beginners to excel at, which was very disappointing coming off the heels of Majora's Mask. I think it's Nintendo's worst main "Big Three" game, and if not for Metroid: Other M, it wouldn't even be close.
Twilight Princess is my favorite of these three. Had the game's side content not been so weak, I probably would have put it up there with one of the very best in the series. Those dungeons are something special.
I think Wind Waker really got the story and themes right. TP and (to a lesser extent) SS had plot lines that I felt were generally messier and not as well thought out. In TP, for instance, the story that kicks off the adventure (Ilia and the kids getting kidnapped) makes absolutely no sense in the grand scheme of things, and no reason for the bad guys suddenly showing up to steal them is ever given. It's just an arbitrary way to get Link to venture outside of his home.
Compare this to TWW's intro. His relationship with his sister is clearly established, then she gets swept away by a giant bird (so far, this is similar to TP). However, we learn later the exact reasons why this development happened, and it makes sense with the game's main villain and the central storyline of the game, rather than being this throwaway moment that is all but forgotten about.
It's arbitrary story moments like these that made TP feel a little more like a collection of ideas without a cohesive whole, and that's something that hurt the game in the long run to me. It did have some excellent dungeons, but in general it was all a little too familiar without adding that element of something new and fresh enough.
SS had its own problems, but I found it charming and "different" enough to still be a worthy game and one of the better Wii titles.
You bring up some good points regarding Wind Waker's plot. I agree that it probably has the best plot of any Zelda game, but I don't play Zelda for the plot. I want a great world and great dungeons, and Wind Waker's dungeons are probably the worst of any 3D Zelda game, so it gets my vote as the worst Zelda game post-N64.
Yeah. Wind Waker had the best story, and arguably the best music too, of the three games. (IMO, anyway) Everything else though...from dungeon design, travel mechanic, Triumph Forks fetch quest, really drag it down.
I'm also not a fan of the art direction in the game either, which was impossible to ignore or overlook when playing the game. For obvious reasons, lol.
It's close between The Wind Waker and Skyward Sword for me. SS had the higher highs but also the lower lows by a long shot. Still, I think as of right now I prefer SS to TWW.
Now, if I were to play TWW HD, I'm thinking that I'd probably have to rank it above SS simply because it pretty much gets rid of almost all my major complaints about TWW, but since I haven't yet played that version, I'm sticking with preferring SS ever so slightly.