10 years ago the answer would have been " FUCKING YES!", but nowadays my answer is Skyward Sword. I know it's very linear and that it holds your hand throught the whole game, but the puzzles, dunegons, story, characters, soundtrack and graphics are still top-notch!

Worst 3D Zelda.
I hope Zelda U does not make easy forgettable dungeons like WW.

WW it is a great solid game. WWHD it is even better in my opinion, the controls are much more fluid, teh visual (of course) are improved... not only because is in HD.
i am so glad they choose this to remake on WiiU!

As for the OP, no, that's Skyward Sword. Best Zelda game since Ocarina of Time.

No. It certainly was back when it was released, even I thought it wasn't as bad as the internet and media made you believe that it was the disaster that destroyed Nintendo, but now it's hailed as the holy grail among Zelda games. Undeservedly so, but that's my humble opinion.

I'd say the most under-appreciated Zelda games are the classic ones (the ones before Ocarina), with the exception of A Link to the Past because that one has a giant reputation, which is mostly justified of course. Zelda II is very under-appreciated, because almost nobody that's still alive now and interested in games played it. The original Zelda suffers from the same, but at least people seem to recognize it's legacy of starting it all.

Link's Awakening however is tremendously under-appreciated. Most people just take that game for granted "because it's 'just' a handheld game", but in reality, it's one of the best games the series has to offer and one of the games ever period.

It sounds really strange that people are giving "most underappreciated" to, insanely, Skyward Sword.

Just shows how out of everyone's mind the handhelds are.

The game doesn't really get worse during the last quest, I'd say. But it does slow down, and you can just tell that there should have been a dungeon or two there instead of the quest you're doing.
The game is still fun during that part if you've enjoyed it up till then. Because it required a lot of sailing around, that was the point in the game I started kind of doing sidequests as I went, and that made it really enjoyable. I'm sure my personal experience can't be replicated by everyone though! I certainly didn't treat the quest urgently, and others might have preferred if it felt a bit faster.

I'd actually say Zelda 2 is the most underrated Zelda game. A lot of people hate that game simply because it is not like all the rest even though at the time, there was only one before it.

All the handheld entries are often overlooked. I think this is because people see LttP as the be-all end-all of top down Zelda. Which just isn't the case! The handheld games deserve your play time too!

Wind Waker is not underrated anymore, people who are fans of it give it the love it deserves and it is talked about plenty.

Zelda 2 is the most under-appreciated. No one even tries to really appreciate it! I feel in terms of discussion it gets relegated out of bounds with the CDi games... but nothing deserves to be counted out with the CDi games.