They don't -have- to do anything. If they wanted to make an OoT2 -- for reasons meaningful or market-driven -- they could revisit the same world as OoT1, or they could set it in an entirely new world. They could depict Link one way, or another. They could do whatever, because it's an ever-evolving series. It's narrow-minded to say they could only design/depict things in certain ways. There was a time in the Zelda fandom when the idea of a title predating OoT would've been laughed at. Likewise for a title revisiting the world of ALttP. Or going from realistic graphics to toon graphics. Or controlling the game entirely with a stylus. And so on.
You're spreading this too thin. Or rather expanding the topic too much, stylus and what would be laughable years ago is besides the point, plus... was it? let's not even go there.
Fact is there are/were internal ideas for OoT and these are not so secret - if anything that cutscene in the middle of TP is "it", that's OoT2 events, they didn't nuke that scenario, they left space for it, but they clearly have an idea of what took place.
And look at that really ambitious E3 2004 trailer, where nothing beyond engine and some gameplay mechanics transited to the final game and you know for a fact that stuff was scrapped, some reused in forceful ways too (that fire temple boss transformation...) but mostly it has nothing to do with the final game. That game surely felt more like OoT, or should I say a OoT sequel.
Anyway, overworld map can't be kept, but the OoT map has to be a strong reference, stuff have to be in the same places, in relation to each other as not enough years have gone by to be able to justify that, but you can change lots of little things drastically. It's not like A Link Between Worlds, but it's not like the OoT to TP difference either, it can't.
And that's also an issue, because instead of a clean state they have to strike for a balance, and trust me, they have.
(I'd also nominate Skyloft in terms of Zelda towns only, but I know that's likely a controversial choice.)
Clearly the best since Majora Mask, but with TP no-show (hyrule town was one of the last things to be done) that's not saying much.
The day night cycle was damn weird, a lot of mechanics in SS have been done better elsewhere, I think it hurt it somewhat. Everytime you want to do something that worked perfectly on some other Zelda and you can't I think it hurts games. They've been running away from musical instruments being a requirement since OoT/MM... WW (although WW was also the start of it), that's a mistake going by the amount of things you could do before and now can't.
They should have kept every song in every game if anything like an easter egg, but keeping an Ocarina or something as a series staple no less.
Anyway, skyloft should have had a "automatic" day night cycle.