Funny thing is that Wind Waker is probably the least polished among the Zelda games, the dungeons were average IMO (I still cannot really remember much about them, except they were bland), and there were only a few. The bosses were fine but like the dungeons there were hardly any, they were vastly more interesting in Majora which did a good job with limited dungeons, likely because it was designed around time restraints. Wind Waker felt unfinished, and the triforce quest is easily the worse padding the Zelda series has ever had and if anything felt thrown in to extend length, it was the triforce scavenger hunt, which was far worse in the Japanese release. People bash TP's overworld but I enjoyed more then the one in Wind Waker, which is quite sparse and uninteresting.
I think Wind Waker the game survives more based on its artistic merits, story, and its battle system. Twilight Princess was an extremely polished game, and I enjoyed most of the dungeons, the story was fine, had some great boss battles along with being the first Zelda game that felt like a true sequel. To see many of the same sights found in OOT, but ravaged by time and war was fantastic.
Did TP have flaws? Of course it did, but Wind Waker had a ton of them as well, right down to being a rushed product. But both games have many redeemable qualities as well. Is TP similar to OOT? Yeah it is but that doesn't mean it is bad, it does plenty to distinguish itself, and I find the similarity in the worlds to be apart of its charm, as a sequel of sorts to the events of OOT. Now if there was another game in the series that felt similar to TP and OOT in regards to setting, I would be far harsher, but as it stands, I find TP to be a great follow up, and homage to OOT. So basically I love Twilight Princess but do not want to see another game similar to it!
Picking my favorite 3D Zelda is still a very hard task, only Majora's Mask and the handheld 3D games did I not enjoy much. With Majora though I admit is a great game but just isn't for me. Now with Skyward I am glad to see nintendo shaking things up, and seemingly implementing great motion controls that actually show why motion controls can be a positive feature for gaming. The game's release can't come quick enough!