Skyward Sword is the worst.
Ocarina of Time can come across as a bit basic nowadays, but it's still a solid game and probably has the meatiest and most broadly satisfying campaign and content, with a good amount of varied dungeons. It's still fun to play even now.
Majora's Mask is a bold, creative game with probably the strongest storytelling and setting of any Zelda, with a strong central theme and mechanic that complement one another. It has a short amount of dungeons and some underwhelming boss fights, but that's about all I can think of in terms of big downsides, the time limit thing is mostly down to personal taste IMO.
Wind Waker is a game that seems to have been rushed and originally had some rather tedious/annoying gameplay elements, notably the triforce shards quest that really bogged down the pace of the game. Nevertheless, it had a charm and energy to it, complemented by its strong visuals and music, that made people much more forgiving of these downsides.
None of the three aforementioned games are in contention for the worst, so it has to be between Twilight Princess and Skyward Sword.
A few years ago, I probably would have said it was TP. It's not a HORRIBLE game by any means; it has its flaws, but overall it's competently made....which is the problem, it's competent but not a whole lot more than that. It just feels kinda "there" and lacks the creative energy and uniqueness of the previous games.
Skyward Sword at least, tries to do something different in a multitude of ways. When I first played it, it stuck out more to me than TP did for sure.
The thing is, looking back on it, I feel that SS and TP are kind of lacking in really big high points, but ultimately SS has bigger and more aggravating flaws that weigh it down. It has worse bosses, a worse overworld, worse enemy variety, it has a worse helper character, the list goes on. SS has a better story but I wouldn't say that story is good enough to be a reason to play the game.
What it comes down to, it's much easier for me to revisit TP and have a fun time than SS, so that's why I think it's the worst between the two. I have never considered it a bad game, but it's just lacking.
Breath of the Wild I have only played for a few hours and as such don't have an informed opinion about it.
Also, maybe it's been too long since I played any of the games in question, but while I can get complaining about Wind Waker or TP's overworld, Skyward Sword's is easily worse than either. It's one of the worst parts of the game.