My favourite game is OoT. My least favourite part? Yes, it's cliche and everyone will jump on me for just sucking at it being the reason I dislike it, but I am going to say it anyway because it's true: I hate the Water Temple. It takes me HOURS even though I've played through the game hundreds of times. I always forget certain keys, I hate changing the water levels, I hate the Iron Boots, and you go through all of that to get to the easiest boss of all the adult dungeons other than the Spirit Temple. Where is the reward in that?
For it being my favourite game, there are quite a few things I dislike about it LOL- I also dislike the Ice Cavern as it feels like a waste of time, I don't like the Biggoron trade sequence because it's tedious, and I hate that you can't really steer Epona whilst using the bow (although this is only relevant to the Big Poe sidequest).
Majora's Mask is a close second, but there is less I dislike about the game. I guess a lot of OoT for me is nostalgia, which is why I love it despite it's flaws. I don't like the save system either, I preferred the normal system used in OoT, which was more fail-safe for people like me who forget and have to redo dungeons millions of times.