Edit: Big thanks to
Razios for providing some quotes from Josh Reynolds about an Alternate Timeline in which Chaos fails. Going to post three of the most important links here, but all of the links are in Razios' post below:
TL
R -
=Kislev obliterated, but Tzarina/IceQueen and loyalists remain in pockets of guerrilla resistance against Chaos
=Auric Bastion and most of the Empire (including Altdorf) get smoked. But outposts and fortresses throughout the battlescarred territory remain. Maybe some cities survive. It can recuperate.
=Bretonnia intact, but most of their knights and Louen died at Altdorf. Green Knight remains Myth-King for a newer, brighter, Francengland.
=Dwarfs are wounded but alive.
=Lizards relocate in their flying Pyramids to Nehekhara -- closer to the setting and revitalizing the region.
=Sylvania is now a force to be reckoned with and takes over as the Big Bad while Chaos recuperates
=Massive beastmen herds remain, roaming the Empire
=Skaven put on the backfoot after losing Pestilens. Managed to wipe out most of Tilea/Estalia/Araby, though
=Ulthuan sunk. Elves united under Malekith, but largely ****ed -- wars to reclaim Naggaroth. Tyrion becomes a roaming warrior trying to redeem himself
=Some Tomb Kings rebel against Nagash
=Orcs rumble back to the Badlands and remain Orcky (why change what's perfect?), some Ogres stick around; others don't.
To add to Reynold's points, I'd say don't have the cultures of Tilea, Estalia, and Araby get totally obliterated. Some hold outs survive against the Skaven onslaught, especially with the Skaven ultimately failing. But what I imagine would be interesting is expanding the strength of Bretonnia with an Errantry War into Estalia and Tilea, which can also fall nicely in line with some historical events in how the French came to dominante Basque (north/east) regions of Spain and Piedmont/Savoy (north-east region of Italy). Bretonnian noblemen going on crusade into the rat-infested warrens and declaring themselves the new kings/princes of ruined cities with Tilean and Estalian populations, much to the local's chagrin.
I still prefer the idea of Nagash and Archaon taking each other out over the incarnates, but if people really don't like it, I can be convinced.