The low point of the Zelda franchise to me was the streak of Majora's Mask, Wind Waker, and Twilight Princess. All three feel rushed and less polished than the other games in the franchise. I still enjoyed two of them, a reasonable amount, but just a lot less than other entries in the series.
Majora's Mask also features my least-liked dungeons in the series, and is very heavy on the recycling. While I also respect what it set out to do and accomplished, a lot of it necessitated things I find inherently unfun. Now games don't have to be "fun", sometimes a deliberate use of that has its worth, but when putting the Zelda games next to each other, I can't help but keep it in mind.
Wind Waker is also rushed, but in a different way than Majora's Mask. Wind Waker feels like they didn't intend to push it on to the shelves yet, but were forced to. I'm guessing the performance of the Gamecube forced their hand. Most of what's there is great, but it has several dips in the game that wrecks any sense of pacing. It also starts with the stealth section, which is the bit that makes me not want to touch the game again.
Twilight Princess, which probably gets my pick for my least liked one, feels rushed in yet another way. This one feels like they were making one game that just never really came together, and they ultimately stitched together with "classic" Zelda staples at the eleventh hour. Seeing as how pretty much nothing of the game's unveiling ended up in the final game, and how the Twilight stuff doesn't go anywhere, I'm guessing it was one of those development hell projects that was just pushed out the door. This is most evident with how it treated its main villain too. Just as you're about to square off with Zant, the undermines him by turning him into a bouncing screaming clown, just so he won't step on the toes of Ganondorf. Ganon was foreshadowed a bit earlier in the game, but essentially had nothing to do with rest of the plot until then. Felt like he was there to check some boxes. This game has no sense of flow at all, from its unbelievably lengthy opening, the constant busywork quests as the wolf, to its back to back dungeons. The dungeons themselves are great actually, some of the best in the series, but I was getting absolutely sick of the game by the time I arrived at the city in the sky, and somehow the game still kept going for hours after that. It also features some of the absolutely ugliest character designs I've ever seen in any game. I can easily see a good game in this, which makes it all the more disappointing to me that it's not. I do give it props for leaning in heavily on the pointer controls of the Wii though. I ended up enjoying that version of the game a bit more.