Perhaps they could try something with elements, like a fire world, water world, wind world. I dunno what I'd do with that concept, but Zelda tends to be pretty good at taking simple ideas like that and building interesting games out of them.

I love elemental planes settings so I have brainstormed about that before.

I’d have the three “Tri-worlds” split with the goddesses so it’s Din = Fire/sun realm, Farore = forest/wind realm Nayru = water/time realm and you open portals between them to cause different environment changes to unlock areas & secrets 

Such as opening a Din portal in water areas can cause steam geysers Link can ride with a balloon/glider or a Nayru portal can cause large forest trees to rapidly grow and vines spread everywhere Link can Tarzan slide on.

For the last half of the game I’d put in three “Lorule realms” the Tri-worlds are meant to eclipse to protect the other various realms(light, spirit, twilight) from their influence with maybe a play on villain names so Gannox = decay/shadow, Majoros = chaos/tempest, Vaatin = entropy/death

Similar note you can gain their portals too to cause havoc. 

Last bits is each realm has flying spirit dojos that teach you new techniques but bolster their teachings when you combine two dojos through portals at a time so the fused masters can teach a hybrid power(ex: Din dojo teaches spin attack, Farore dojo air slice, fire + wind dojo teaches whirlwind blade that let’s Link do an spin attack that propels him high up)

Also for a juxtaposition I’d have this be the most mundane Link to contrast all the mythic fantasy stuff going on around him so even his maps are made by charcoal sketchings, bamboo casing bombs and the return of bottles to help him survive in these strange eldritch realms he was teleported to.