Personally, I don't think any of the clues in AoL were too cryptic to figure out without a guide, but I do agree that some of the clues could use additional clarification (or additional hints in themselves).

There are a few places where something would be hidden and no clue would be offered at all; the game just expects you to stumble upon those secrets by yourself. That made sense for the NES days, but would probably feel a bit too antiquated for most modern-day gamers. So a remake would definitely do well with more clues and clearer clues.

If a remake included Rupees, you could use that for various items like Repels, Health and Magic potions, maybe Experience enhancers, some Itemfinder-esque item that would point out secret areas on the overworld to you. I think there's enough that could be introduced into a remake to make a Market a good addition to the game.

I think the most important parts of AoL that a remake would have to retain though are the combat (which necessitates either the same 2-D combat screen system or a much more in-depth control scheme than what we normally get for traditional Zelda combat), the spells (which could encourage the remake to employ more need for the spells, like how in the Game Grumps playthrough they almost never used the Fire, Spell, or Thunder spells outside of when they were necessary), and the labyrinth-like setup of the dungeons. Maybe the dungeons could include a Metroid-style map that filled itself out as you progressed, which would help ease new players into AoL's style of doing dungeons.

And I would love it if an AoL remake could actually wrap up the story. The Game Grumps playthrough never really mentioned the story since it was primarily contained within the game's instruction manual, but the game ends with two major plot points unresolved: the fact that Ganon's minions are still after Link's blood in order to revive Ganon, and Link waking up the ancient Zelda means there are now two Princess Zeldas alive simultaneously (so what does that mean for the throne of Hyrule?). And there's also a minor unresolved plot point about how the ancient Zelda knew some secret about the Triforce and refused to reveal it to her brother, but that may be nothing important (particularly if that secret was just about where the King had hidden the Triforce of Courage).