although I do agree with a lot of your opinions, I wouldn't say WORST.
the plot is probably one of the best in the series, and even though the game had a lot of bad things in it, I found it fun enough to not be my least favorite. I just didn't like the lack of exploration, the sky is probably what disappointed me the most. I would of been okay with the small city in the sky if only there was more to explore up above! Maybe even more cities?
(random rant)I liked the islands in the wind waker 'cause I could actually had to figure out something! The wind waker was so much more fun BECAUSE of the islands in it, the only way wind waker could of been more exploration-ish(?) is if there were more islands in between and/or bigger ones. I thought too my self when I heard about the sky is "hey! I bet they fixed the problem they did in wind waker! yay! more exploration!" But no. It was the biggest disappointment to me, that and a few other things is why this game isn't my favorite... But I can't say its my least favorite 3D, 'cause it was more fun then TP, and that's it. It was more fun! :]
The reason why I liked this game better then TP is because of its fun innovations, the boss fights were harder, no disappointing main villain, the over world was less boring, the enemies were more fun and even though Zelda didn't do anything in the main boss fight(which I find a stupid thing to complain about anyways) she was more then just a damsel in distress, she became a very important component to the plot and is your best friend.
And the thing about the cities? I'm with you on that one, dude. With the people needing to be up above the clouds for so long(which was already a whole civilization before they went up to the sky), you would think they would have children. I know they wanted to concentrate on the 'characters', but they did a terrible job. I found all the characters personalities generic. Even if clock town didn't have THAT many people in it in reality, they sure made it feel like there was! So many ways to make the characters deeper then they were, if they did that I think the town might of felt a bit larger. This also brings me back to the lack of sky there was, ugh. they could of made the world so much more lively if they had more people and more towns in the sky!
So yeah, I agree with you... Sorta. I found the dungeons some of the best in the series though, thats another reason why its not my LEAST favorite, it made up with its fun-ness. But if it lacked the wonderful gameplay and amazing plot(for Zelda) this game would be my least favorite.
Even though my complaints seem harsh, in reality they could be easily fixed. They just needed to think deeper in the characters lives, added more exploration, and more people(I don't care if there is a few characters that just repeat what they say when you talk to them) To be honest, the way the characters evolved was interesting, I liked how things changed as you went on your quest, that made the characters seem more alive, they just had cheesy personalities and problems with unsatisfying outcomes.