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.