Great insight! Going to list our locations based on what you've written. Items separated by a // are considered parallels. Items separated by a comma cohabit the same region.Hyrule Desert - Castle town underground, sewers, maybe a light car subway system? Prisons and torture chambers? I think we'd also mentioned that the Gorons might be mining in this area?
Maro Woods - Underground jungle. The magmatic activity has led to the underground being fertile and warm in many parts of Hyrule, here the forestry has begun growing downwards as the surface is now dominated by the Maro
Eldin Caldera - Magma chambers, I think on the outskirts of this, i.e. around where Kakariko would have been would be a good location for the Sheikah village?
Fissure Falls - Water caverns, new home of the Zora
Lake Hylia - Still aren't 100% sure what we're doing with this on the surface...maybe the other faction of Zora has moved into the remains of the water temple, causing the rift because the remaining Zora consider it an act of blasphemy?
Gerudo Swamp - Ice grotto, being one of the further regions from the Eldin magma chambers this is a fairly cold area, moisture from the swamp seeps into the earth and creates a frozen labyrinth, new home to the Gerudo. Maybe being deep beneath the surface, relics of Lanayru Sand Sea that were buried by the sands could still be frozen into the caverns
Snowpeak
Great Hyrule Canyon - I blanked on both of these for now, Snowpeak would be obvious but it is redundant with my idea for Gerudo swamp
Also would like to work the names Faron and Lanayru in here somewhere, things named Lanayru tend to be amazing for some reason. Though Eldin Caldera being the only reference makes sense too, this is a Hyrule brutally transformed by the raw power of nature, human virtues like courage and wisdom are gone
An expansion on the subway idea: Hyrule railroad. When you first explore it it's derelict and dysfunctional, a hazy stretch of tunnels the connects various parts of the land, each region would have multiple stations where they intersect with it. When you get the Master Sword hilt, you're able to use the rails and can use this as the method of quick travel, instantly transporting you from station to station
Overworld // Underworld
Goron City, Hyrule Desert // Goron Mines, Hyrule Tunnels, Temple of Time
Eldin Caldera // Dodongo Caverns, Zelda
Fissure Falls // Zora's Domain
Great Hyrule Canyon (weaves in an out of the over/underworlds)
Lake Hylia...
Maro Woods // Deku Jungle
Gerudo Swamp // Sunken Glacier
...
Gotta crash. Going to the Zelda symphony in Dallas tomorrow.