Spirit Tracks and Twilight Princess both come close, but I'm not quite sure which one I dislike more.
Twilight Princess's storyline seems sloppy and in some parts, just thrown together without much thought. The appearance of Ganondorf was only because Nintendo thought "No Zelda game will ever be better than Ocarina of Time without Ganondorf." Zant was an awesome villain, then Ganon came in and killed him off, basically. If Nintendo was going to build him up so much, then they shouldn't have given him a really, really crappy and lazy boss fight, then kill him off like that. He could've had an awesome boss fight, but he just copied what previous bosses you fought had done.
The gameplay is too similar to other games for me. The Slingshot was only thrown in there for really no reason at all. It is an extremely weak, extremely short-range item. To make it worse, you get the Bow in the next dungeon, completely rendering it obsolete. If the bow were to replace it in the inventory, then I probably wouldn't have as big of an issue with it, but for about 95% of the game, it's just sitting there. The Motion Controls were really sloppy as well. You could tell that this wasn't planned for the Wii. The swinging of the sword idea is interesting (and obvious) but they didn't pull it off well. It gets kinda tiring doing that, and late at night, when I normally play games, I'm kinda tired and don't want to move my body around much. I wish there was an alternative control method where a button would swing the sword, as opposed to being forced to use the Motion Controls.
Now, with Spirit Tracks, there are quite a few things I hated.
The train. It's slow, it's not very innovative and what they did innovate on made it worse. They really took out the "Open Overworld"-ish feel away from Zelda, especially Phantom Hourglass where you drew your course instead of being forced to rails. The rails added some interesting collectibles, but they weren't interesting enough to make up for the disappointment the train brought. The method of acquiring train parts is just annoying. The treasure system is flawed to where it's impossible to get every train part in the game realistically. Stumbling across Ship Parts in PH was fun for me, and buying them from Beedle when I wanted to, that was also fun. They were easier to get, and more fun to come across. Not saying I don't like a challenge, but with the Train Parts, they're mostly just luck.
The Tower of Spirits, I know a lot of people liked it over the Temple of the Ocean King, but it was just annoying for me. The Phantom Zelda idea was just broken. Her controls were hard to use and for the most part didn't work well at all. She wasn't fun to have around and she was in the way most of the time. Having to control two people at once in a fight is hard, and not in the fun way. In the way where it's just unnecessarily aggravating.
Still on the Tower of Spirits, while I'm glad we don't have to replay parts of the temple, the speed element and the fact that every time you went through it opened up new paths, made it a lot of fun for me. Every time I went through, I have a new item I had acquired in the previous dungeon that opened up new shortcuts, alternative paths and so on. This added diversity and made it fun where I still had to figure out what to do, even on the floors I had played before.