An important factor, is that ZC is no longer the only game in town. I'm unsure if @DarkDragon has looked at the Solarus engine. IMO, that is the right direction for ZC3. Every object in Solarus is scripted... If you went that route, and you had easy to use attribute editors so that scripting is not a mandatory requirement to use the flipping thing (note that Solarus does not yet do that, but it's on @Christopho ' s plan), you would have something that can hold up to the test of time.
I'm not aware of Solarus, though I played Megazeux back in the day, which also was a fully-scripted engine on top of which all of the game elements were built. It's a very tempting model, especially to us computer scientists who will abstract anything given the slightest temptation.

However! I will warn you that I traveled quite a distance down this path 5-6 years ago when we were first pondering the idea of a full remake, and an "everything-scripted" Zelda remake would require a **lot** of thought and pre-planning to have any hope of success. Just think of what a Link script would have to look like, so that he correctly transitions between all of his possible states in LoZ -- walking, attacking, hurt, dying, rafting, on a ladder, warping, etc etc etc) -- and responds correctly to user input and world interaction in all states. I don't know how Solarus is built to manage the complexity, but I'd imagine a sophisticated message-passage system (perhaps along the lines of, but far more elaborate than, MZX's system) of some sort would be needed.