1.  The Legend of Zelda (NES) - Simply the most groundbreaking game ever made at the time of its release, made even better with the inclusion of the second quest.  Whereas some great classics, such as SMB and Metroid, had very welcome improvements made regarding play control or hit detection, the original Zelda still plays flawlessly today.

2.  A Link to the Past (SNES) - A close second to original, it has aged beautifully and can swap places with #1 depending on how I critique them.

After this it's much more difficult to list them.  Ocarina would probably get my vote for third, with BOTW and Majora's Mask pretty much tied for 4th.  And Wind Waker would be next; even higher, in fact, if only it felt more complete.

Regarding BOTW2, I hope that it has more traditional Zelda dungeons.  That was the main problem I had with the first - the Divine Beasts and Hyrule Castle all felt lacking compared to dungeons and temples in earlier installments.

Breath of the Wild is an underrated classic.

Hard to choose between BotW and Windwaker. For now I'll stick to windwaker as I've double dipped and played through it at least 3 times from start to finish, a rarity for me. BotW is amazing yet so far I've not felt the urge to play it again.

There are still lots of people, even in this very thread, who keep denying that it is the best game ever made. So yes, I'd say it's perfectly reasonable to call it underrated.

The Wind Waker, hasn't really changed ever since I played it

Bonus: More focus on the story, even if that means adding linearity in the game

This reminds me of that Youtube video where that guy is all like "Why doesn't everyone RECOGNIZE Nier Automata as a perfect game?? Why aren't gaming journalists covering this as a perfect game when all of these same people are giving it praise like it is one??? If you all are praising it so much why don't you give it 10/10s across the boards???". This wasn't from some random guy but rather a Youtube reviewer gone somewhat professional game reviewer named Skill Up (at least I believe it was him because the thumbnail and title and his voice sound pretty similar from what I remember). 

Then you play the game and it's like ... yea ... the positives the reviews mentioned weren't wrong. But there's a ton of reasons why it isn't a perfect or 10/10 (since those aren't necessarily the same thing) game. 

Lol not to go on a rant, it's just funny to me that someone who is basically a real game reviewer now has a video on their channel basically complaining that reviewers didn't overrate a game enough. Sometimes talk feels that way about BOTW. It's an amazing game but it doesn't necessarily need to be considered the best one ever  

on the botw 2 subject I would like to see a more vibrant world in terms of characters and enemy types . I also found it to really open up when I had the ancient armor and weapons but it took to long, to get to that point.

Breath of the Wild
Legend of Zelda
Zelda 2
Link to the past

Bonus: I hope BotW 2 uses Hyrule Castle as a blueprint for its dungeons. If my wish comes true, oh boy will I be excited. 

Botw 2 can use longer dungeons and less repetitive shrines. Quality over quantity. The 'challenge' ones got pretty boring towards the end. It would also be nice not to have a choke point for essential upgrades, like the inventory slots. I didn't find the guy until 80 hours in, since I went my own way. Better enemy scaling, the castle was awesome to explore early on. When I went back to finish the game it was a cakewalk, anti climactic.

I would also like to see time travel used again as a game play mechanic and more underground / underwater exploration.

Twilight Princess remains special to me because it's the first one I played. I love its art, too. Still, I think Wind Waker is the best game in the series.