So I'm playing Zelda Ocarina of Time for the first time and holy crap having to go into this menu to equip/unequip these boots which are a game mechanic for an entire dungeon is goddam awful. I understand they fixed it in newer versions, rightly so. I'm powering through it but urgh.
Not much else springs to mind off the top of my head. More the inability to do something, such as selecting multiple units using click and drag in RTS. I replayed Dune II a few years ago and not being able to do that was frustrating.