I'm not sure how well received this idea would be, but what if instead of exploring a world like in a Zelda game, you instead go through stages?
Okay, but hear me out. These stages can have various routes, and connect to other paths in other stages. This means you could theoretically take several routes through the same game, finding the most enjoyable/ fastest/ coolest route. Backtracking is discouraged, and in some cases impossible, more on this later. You could even take it a step further, and get rid of the way items are traditionally used. Instead of the "find item, get boss key, beat boss" approach, different stages could have you use different items that you either start with, or find. This might not make sense from a story standpoint, cause why are you losing everything between stages, but anyway, it could be fun. You start a level with the Sword, Bow, Bombs, but you will need to find either the hookshot, or candle to progress. You would always have a few items, and there might even be a way to keep items, but this will depend on the level design themselves. Really, it's pretty much how FSA did it, except you can have more than one sub-item. The story could be made around this too, if that's your thing. There could be reasons why you'd take a different path. You'd meet different characters, etc. Losing items could be explained as 'traveling through different dimensions' or something else dumb like that.
EDIT: I was also thinking it would be cool to have the player choose one of two characters at the beginning. Different sprites are simple enough to implement with a dummy item and LTMs, but you could take it a step further, and make them play slightly differently too. You wouldn't really need a script for this either, but it would be pretty simplistic. Basically, whichever character you choose uses its own d-maps for the stages which will have certain items either on, or off. For example, char1 can use the bow, but char2 can use the wand. One has regular bombs, two has remote bombs. One takes more damage while dealing more damage, and one has higher defense, but weaker attacks, or some such variants. This is something relatively simple (Okay, not really once you get into the logistics of setting up the d-maps, and subscreens) but I think it could be fun. If you wanted to go the scripting route, the sky is the limit. What I'd do is have it so that once you clear the game with one character, you can play through again with all the items you'd have found, and do a new game+ type of thing. Beating it with both characters allows either character to use ALL items (even ones they wouldn't normally have).
Would anyone here like a quest like that, assuming it was actually fun, and not a linear slog through uninspired areas? What if each level looked different, and had a different goal. You weren't just palette swapping areas, but instead, adding new puzzles, themes, enemies and hazards? The answer is probably yes, but I dunno. I know that people like there ZC a certain way, and ain't nobody gonna tell them otherwise