For me, it's not that I didn't enjoy the 3D Zeldas, sans the original Ocarina of Time. I actually loved each one. Let me explain:
Ocarina of Time N64 - I simply didn't like how the controls felt. Very clunky and floaty. And the framerate annoyed me. I realise that it's an old game, but that doesn't change the fact that those elements pulled me out of an otherwise fantastic game. I also find it to be a game with a very slow start. The original version of this game simply hasn't aged all that well.
Majora's Mask - The controls were better here, and the framerate didn't bother me as much, if at all (even though it's not much better, IIRC). I actually really want to go back to this one, it's one of the more fascinating Zelda titles. The only problem was, when I started my playthrough of this, I was quite sick. My train of thought was very slow, and I felt very drained. Therefore, I was far too indecisive and couldn't really handle the more stressful nature of this game. I booted it up on my emulator thinking it would be like other Zelda games, where you can take your time if you wish. I was dead wrong.
Wind Waker - My brother got a lend of his friend's GameCube and this game, along with some others. I played a fair bit into it, but we gave back the borrowed items before long. So I never did get a chance to complete it.
Twilight Princess - I was at the point in the game where you go to the desert dungeon. I was going on a Heart Piece hunt before heading there (simply because the fortune teller in Hyrule Castle Town meant this was easier to do, so I got hooked on finding them. I love finding collectibles in games), along with other side quests. However, my little cousin was over one day, while I was out of the house. He wanted to try out the game, and wound up deleting my save file. Wasn't bothered going back to it. This was a few years ago, so it's probably high time I start the game again.
Phantom Hourglass/Spirit Tracks - I just.....dropped them, for some reason? I can't remember why I stopped playing them. I was having fun with them, then I just stopped playing for whatever reason. I have no idea why.
Ocarina of Time 3D - They fixed the problems I had with the original, sans the slow start (though that was much less of an issue because everything else was better than before). However, I simply got stuck on the fourth dungeon, the Forest Temple. I still have my save file, and the game. But I was stuck in a "TRY EVERYTHING, WITH EVERYTHING, ON EVERYTHING, USING EVERYTHING" kind of way. Like, I was progressing fine, and suddenly, there were no new areas I could visit. There was a balcony I could see with a chest, likely containing a small key (which I needed). I couldn't find my way up, though.
I think it's funny, because I do love the Zelda games. I wouldn't of played nearly every game in the series if I didn't. But I seem to always have terrible luck with the 3D titles. I have finished most of the 2D games, though.