It seems to me that the biggest challenge lore-wise to having the three factions fluffy enough is what you have some factions that *hate* another faction (eg Dwarfs hate Greenskins, Empire hate Chaos) so it seems the only way to deal with that depends on which of these two scenarios is happening:
* when one factions has only one faction that it hates (may be this is Empire hating Chaos, and may be Dwarfs hating Greenskins but this isn't the case anymore for the last edition of WFB see below?) split up the hated faction (so Chaos gets split into its most common alliance: Khorne and Nurgle versus Tzeentch and Slaanesh, OR if we want to go for Chaos Undiviided then Chaos Warriors versus Demons of Chaos)
* when one factions has multiple factions that it hates (this would be if we agree that Dwarfs hate: Greenskins and Skaven as per the last edition of WFB, and I think to some degree Chaos Dwarfs) then they should be split into evenly hated blocks (which I think would be: Greenskins because they seem to be hated as least as much as the others, versus Skaven and Chaos Dwarfs).
To me, this would suggest these groups (but there may be other hatreds that conflict with this scheme, and this would put an emphasis on some, over other, particular aspects of: each Chaos god, and Chaos Warriors and versus Chaos Demons):
* Order/Preservation/Goodish Block: Empire, Dwarfs, High Elves, Wood Elves, Lizardmen, Bretonnia.
* The Destruction/Entropy/Exterminaton Block: Khorne + Nurgle Or Chaos Warriors, Greenskins, Beastmen, Ogres
* The Corruption/Domination/Scheming Block: Tzeentch + Slaanesh OR Chaos Demons, Skaven, Chaos Dwarfs, , Dark Elves
Be coold to hear others' ideas and better ways to divide the factions!




