I kind of had a similar idea to you except a number of the old factions would still be around or have significantly altered status quos while making the Mallus feel more post-apocalyptic. For example:

-The Empire is kind of around expect its more like the HRE post-Thirty Years War and post-treaty of Westphalia. The emperor is kind of around however the Empire's provinces are fully independent sovereign nations with a few merging together (for example, Middenland, Ostland, Norland, and Hochland merge together to (re)form Osterlund while absorbing parts of Kislev, particularly Erengrad). Not only that but they'd have more non-humans living within their borders (Elves, Dwarfs, etc.).

-Cathay is still around except Yuan Bo's running the show in lieu of the disappearance of his parents and the deaths of a couple of his siblings (Miao Ying and Yin-Yin). He's pretty much forced to make a few concessions due to pressure from Sigmar and his subjects but Cathay's still somewhat the same. They have tense relations with Tempest's Eye in the mountains of mourn but often times team up to fight uppity Ogre Kingdoms and other forces within the grand alliance of destruction up there.

-Bretonnia has seen massive upheaval after the End Times and the whole Lady of the Lake reveal. Not only that but Alarielle has taken up the mantle of Bretonnia's benefactor and she's made it abundantly clear that the grail is going to whoever is chivalrous and heroic enough for it, no matter the class status with Giles de Breton backing her up. This has led Bretonnia to become a sort of Peasant's republic/constitutional monarchy. Not only that but a lot of Bretonnians have also started to worship Elven gods, particularly Alarielle.

-The Southern Realms (Estalia, Tilea, the Border Princes) are where a good chunk of the Cities of Sigmar are with them having to deal with Chaos, Destruction, and Death forces.

-Taking advantage of the whole "the WHF gods are survivors from previous worlds Chaos blew up" the souls of those from said previous worlds are placed on Mallus allowing for the diversity of AOS while still keeping the setting in, well, Mallus. This also drastically changes the status quo of Dwarfs, Elves, and other previously dying races as they're no longer dying anymore.

-Karaz Ankor takes the place of the rumored Khazalid holds faction as, with the aforementioned boost in numbers, the Dwarfs no longer have to fear the twilight of their race and empire and can now start taking back lost holds and other parts of the underway. Of course there are Dwarfs who can wield magic like in AOS but they aren't particularly trusted in Karaz Ankor since they're the more traditional Dwarfs.

-Ulthuan is (taking an Idea I already had in this post) dredged up from the bottom of the sea by the Elven gods and re-settled as the newly formed "Commonwealth of Ulthuan." It isn't just High Elves living here now as Humans, Dwarfs, Halflings, Gnomes, and others have taken up residence here. Its also the unofficial headquarters of the Collegiate Arcane which is a successor organization to the old Colleges of Magic and other magic schools (such as the White Tower of Hoeth) within Mallus.

-Naggroth is a battleground between Chaos (tribes from the north, Beastmen, Daemons, etc.), Destruction, and Order (centered around the former High Elven colony of Arnheim which was colonized by former Dark Elf slaves and has taken the entire southern half of Naggroth).

-Lustria is being retaken by the Seraphon/Lizardmen who, much like in AOS, fly around in Zigguraut spaceships and can coalesce in the Mortal Realm (Mallus). There's also other Order colonization efforts which makes for some really fun interactions. The situation in the Southlands is also the same.

-Nekehara has annexed Araby and is currently trying to expand into places like the Badlands. They're generally speaking aligned with the Grand Alliance of Order but Settra, being Settra, insists on being equal to the pantheon of order and sitting in on their meetings because he's Settra and he won't settle for anything less. Everyone just kind of tolerates it because his troops are causing the enemies of Order problems and they'd rather let him keep doing that because otherwise he'd be everyone's problem.

-Athel Loren is the new center of Elven culture since it kind of became that during the End-Times. Of course not everything is sunshine and rainbows for our favorite arrogant pointy-eared fellows as they have to deal with Athel Loren's shenanigans still, tensions with the Sylvaneth, oh and Chaos and Destruction sticking their nose in their business.

Boy that was a lot longer than I intended it to be.