Can't beat the original. It has the freedom level of BotW with better combat and better dungeons.

Bonus: My hope for BotW2 is that it keeps the overworld and physics engine of BotW while adding several dungeons that were as cool as Hyrule Castle. My expectation, however, is that it won't be as good as BotW.

Skyward Sword for me. Best story, best combat, best dungeons, and the period from the start of the Ancient Cistern until the end of the Pirate Ship, including sailing on the sand sea, are the best 10 hours of any story-driven game I've ever played.

Top 5: 

1.- Ocarina of Time

2.- A Link to the Past

3.- Breath of the Wild 

4.- Twilight Princess

5.- Majora's Mask

Tbh, my #1 and #2 are basically interchangeable, as are my #3 and my #4, as I love them pretty much the same, so I guess you could consider them tied. 

Bonus:

First and most important: MUCH more enemy variety. As good as BOTW is, that was a big let down for me. I expect and hope BOTW2 to fix that. 
Second to that, I honesty just expect it to be have the same or similar quality - which is to say, I expect it to be a great game.

Something I'd like, but dont really expect is a more elaborate combat system and an entirely different weapon durability and item storage systems. Those would be much appreciated.

The first one, chased by the BoTW

I'll give you the full rundown:

1. Breath of the Wild
2. Twilight Princess & Majora's Mask (Can never decide between these two)
3. Ocarina of Time
4. The Wind Waker
5. A Link to the Past
6. Skyward Sword
7. The Legend of Zelda (NES)

The others I haven't played.

Wind Waker by far.

Not really sure. Ocarina of Time has the consistently best dungeons and a pretty neat world, but I kind of ruined my first playthrough by not getting Epona/not realizing that the map literally tells you where to go.

Wind Waker has the best artstyle overall and feels like the Zelda game with the best identity, but also I didn't even finish it because of the Triforce quest and parts of it felt a little aimless.

A Link to the Past has the most killer least filler, but it's highs also aren't as high as the rest of the series for the most part and while I think it does what it wants to do really well, it does have probably the most basic identity of any of the Zelda games. 

Majora's Mask is great, and should be my favorite by far, but I really didn't like the last temple, find the Pirate area pretty annoying, and just got frustrated at certain sidequests right towards the end of my playthrough, which left me a little bitter. I think some of it's sidequests can be a little too directionless in an annoying way, which is frustrating because Clocktown exists as a way to mostly alleviate that criticism since so much of the sidequests happen naturally otherwise.

Breath of the Wild really doesn't have any "inherent" problems, it's just that it's content is incredibly basic and a lot of the best parts are spread a little thin. But the game mechanics and world (although somewhat empty at times) are mostly great. It's OST also isn't that great.

It's a toss up, but I think ALTTP, Majora's Mask, BOTW and Wind Waker are the ones that are most likely to be my favorite. I'd have to replay them to have a final opinion. I guess I'll vote MM.

Oh, and I almost forgot, Link's Awakening is a cute little game, but it's not even in the running. 

Breath Of the Wild with OoT a close second

and I hope and expect dungeons in the sequel

Ok for the sake of argument, I am voting based on traditional Zelda games. BotW is a game I absolutely love, one of my favorite games of all time. However I don't feel right putting it up against the others being so different (despite being inspired by Zelda 1).

So with that, A Link to the Past is the pinnacle of the traditional formula. It set the ground work for the traditional formula far more than Ocarina ever did, and is densely packed with content. My favorite 3D Zeldas from the traditional formula would have to be Twilight Princess or Majora's Mask. Right behind them is Skyward Sword (so yes I am excited to play that again on Switch).

Mine too, funnily enough.