So... Emperor Vlad vs Sigmar? That would be fun.
But my idea is more than anything to scrap the End Times alltogether, except for the good parts: the Sundering of Ulthuan and Malekith as Eternal King, the fall of half of the Empire (poor Ostland, their uniforms colors were awesome), to make the stakes go up (and to make Mordheim's scope of play more extended!), and also the resurrection of Nagash was a neat concept, as well as having Vlad re-instated as Elector Count, I loved that part. They didn't do much with it, but it was cool.
I'd be in favour of killing off most of the important guys save from Gelt, Todbringer, Schwartzhelm and Helborg. The first two, becauser they can lead different Empire factions with their own personalities. The last two, because they've been a dynamic duo of bro force old sods for almost 20 years now. And how nice are their moustaches!
This is what I've imagined. Yes, I've got too much free time.
You've got a very martial-oriented, totalitarian Todbringer, Ulrican empire; a very religiously crazed Empire officially under Liutpold but really under Volkmar (after all, these were
really almost the End Times!) and a steampunk / Gold Magic Empire led from Nuln and Averheim with a specially strong devotion to machinery (and magical machinery!). Which means, of course, clockwork golems. Wouldn't you buy them minis? I would!
Granted, this is very Empire-centric. But I am an old Empire player. I can't help it.