Having read similar suggestions, I've decided to throw in my own one for Toady to view or even consider.
With upcoming magic/myth update, it could be natural to, as topic says, add different co-existing planes of existence and instead of creating a single world generate a whole multiverse.
So, there are a few things to note about this and several ways to implement.
First of all, the planes are generated simultaneously. It's not about merging already existing worlds. The easiest option is to make the worlds share the same raws, more complex solution: use different sets of them, saving them and using some additional markings to, for example, distinguish the dwarves of plane A from a little different ones of plane B.
While you can simply make a couple (or even dozens) of worlds with the same world constants (or maybe even the same terrain seed, for maximal parallelism), you can, at the cost of memory and probably some speed (in addition to obvious FPS loss due to simultaneous processing of a number of worlds), have conflict-free multiverse with the potential of planar travel, which may be added in magic updates.
How will this work for us, users?
At multiverse generation screen we might have an option to add planes, each using its own specific set of raws (and the sets may be shared as I've mentioned above) and other settings (like high-fantasy/low-fantasy that Toady promised for myth update and, of course, the init settings). These sets are then added to the multiverse folder and are used by the game when playing this muliverse.
But there's more. This concept may be improved by generating special planes with unusual properties automatically. Like something similar to astral plane in D&D multiverse. Or whatever else.
The main idea is to make different planes with different gods, civilizations and histories, and allowing mages and magical entities to open portals between them. This may lead to a lot of fun when your fortress mage opens a gateway to a plane dominated by clowns. Or a plane where there are no dwarves, only humans fighting goblins, both races stuck at bronze age and will pay tons of gold for steel weapons.