That guy isn't even from Windwaker.
I'd argue Twilight Princess doesn't even have the best dungeons in the 3D games (MM imo), much less the 2D ones. I also don't think they are "far better" than Wind Waker's, and that's kind of a problem I have with all the 3D games as a whole: outside of a few instances, the dungeons are typically so streamlined and simple that none of them really stick out to me or provide a ton of enjoyment. I can tell WW's are more linear and easier, but I can't say I wasn't really having any less or more fun with them, for better or worse. That's why seeing Mark Brown's
Boss Keys videos were really enlightening to me, because it always feels like I'm just blasting through them and going through the motions so it's hard to take a critical eye to them.
As far as the overworld goes, Wind Waker is the only 3D game where I felt like I was actually exploring, even if some of that feeling is emulated. I also thought combat and control are both better than TP. Then there's the art direction, atmosphere, characters, etc.. I like Zelda games because they are greater than the sum of their parts, and that's ultimately where WW surpasses the other games for me. Obviously I didn't get too analytical here, but personally and judging from other posts in this thread it's pretty clear that no, TP is not definitely better.
Also if it wasn't obvious enough from that last paragraph, I haven't played BotW yet.