So, we all know this game is the best in the series, and that it is damn near perfect. But everything has flaws, and everything can be improved. So what are some issues with Link to the Past?
1. While the game does encourage a sense of exploration, much of what you discover becomes pointless on a second play through. There are caves and holes with nothing better in them than a few rupees or some health. (Although it could be argued that discovery is only fun if exploration sometimes fails to produce anything interesting.)
2. The fairy pools are useless. (See point 1.) Aside from the two who upgrade your items for you, all they do is restore your health. I never really find that I need more health than can be found under bushes and such.
3. The invisibility cloak and the blue cane are pretty much identical, and they both use up MP so fast that they're almost useless.
4. The Skull dungeon (Dark world, 3rd crystal) is one giant "fuck you" to the player. Some parts of it are actually really interesting and well designed, like the fact that it has numerous entrances, or the fact that the final enemy in the dungeon is in a completely separate area. But the constant stream of wallmasters is frustrating. And, worse yet, huge portions of the dungeon have no purpose whatsoever. They're just there to waste your time. If you know what you're doing, you can skip 50% of the dungeon.
5. The dash function is so integral to the experience of the game, that on any replay, it's incredibly frustrating to not have them prior to finishing the first dungeon.