Though OoT is quite high in my list of favourite Zelda games (I only like aLttP and MM more) there are some things that annoyed me a bit:
- The very slow introduction: Before facing off your first enemy, you have to watch a long cutscene, look for a sword and grind for lots of rupees for a shield. Then there are just a few pathetic Deku Babas and you have to witness another long cutscene before you can finally enter the first dungeon which also has few weak enemies. This takes about 15-20 minutes. If you're used to earlier Zelda games this gets boring. Fx in aLttP, you already face a lot of enemies in Hyrule castle when you're about 2 minutes into the game (and you can easily die there if you're not careful), you simply have to leave your house, walk up to the castle, get your sword and you're all set and ready to go.
- The emptiness of the overworld, especially Hyrule Field. No enemies besides some random peahats and stalchildren at night, only a few trees scattered around the place and a small brook, all that in a huge field. Even TP's often-critizised large overworld didn't feel that empty to me. Again, this is probably me being used to the highly vivid and diversed overworld of aLttP. But hey, it was the first 3D Zelda so you wouldn't expect everything to be perfect, MM already did a much better job with that.
Minor:
- As many of you already said, getting from A to B as child Link takes ages because there's no warping or Epona or even a functional Bunny Hood. The time between first leaving Kokiri Forest and reaching Castle Town before dawn was calculated very tightly (you could make it in time by rolling though). They could've done it like in aLttP (at least in the Light World) and let you choose to start from certain different places you've already visited before.
- Navi's constant reminders about going to the next dungeon when you're on a sidequest. Let me do my sidequest already, the dungeon can wait, K? And her Captain Obvious-like behaviour in the first dungeon ("You can climb up vines!/open doors!" etc.)
- Kaepora Gaebora's senseless, redundant and unskippable "information"
- The iron boots and the way they had to be equipped
On that occasion I have to add that for me, the Water Temple was one of the high points of the entire game, finally a dungeon that made full use of the 3D and where you had to think a little to advance. I'll really really hate Nintendo if they water it down (no pun intended) in the 3DS release. They should just make the iron boots a C-Button item or otherwise easier to switch on/off but they should not turn the Water Temple into an easy-peasy cakewalk just to please every last preschooler that might toss the game aside if it isn't 100% linear and some backtracking is needed.
