Oh boy, there's a lot I don't like about OoT.
But the worst of them is the not-so-user-friendly menu. It's so annoying to have to press START, move over to the screen you want to use, and then select the item. Doing it a couple times isn't so bad, but you have to do it constantly throughout the game. The Water Temple is infamous mostly for this reason, forcing you to constantly switch between the Kokiri and Iron Boots, and other parts that make you switch between equipment, like the Shadow Temple with the Hover Boots, or having to switch to the Hylian Shield to deflect projectiles, then Mirror Shield for...everything else once you have it. (It's the same thing with Child Link, since Hylian Shield can't deflect projectiles as a child and Deku Shield can, well, burn).
On a related note, only having three C-buttons and a lot more than three things you need to put on them is annoying. Slingshot/Bow, Hookshots/Boomerang, the Ocarina, elemental arrows, Bombs and Bombchus, Lens of Truth, Bottles, the items in the Trading Sequences, Megaton Hammer, spells, etc, etc. You need most of the items you can equip to C, and having to switch between them over and over (and sometimes accidentally using the wrong item because you normally have something else in its place--I once wasted my Fairy because the Longshot was normally on that C button) is annoying
*end wallpost*