While I don't have anything against that, it could be different side by side. Instead of Men and Fallen have each 6 factions, Men could have 6 and Fallen just 3 but these 3 be more variable/different. It would be more in-deth, allows for better storytelling, leting things more realistic (immersive) and less symmetric. Games tends to follow these symmetrical correlations a lot, would be likeable to change.
The Fallen are derivative of men.
From a game mechanic point of view, The Fallen make use of death magic, Men make use of life magic. It's not so much a good/evil thing as it is the worship of death vs. the worship of life.
When Fallen civilizations territory expands, the landscape changes to be twisted and deadly and Fallen Civilizaitons get a significant combat bonus versus Men on those territories. By contrast, when the kingdoms of men expand, life is returned to the world.
Or put another way, the world of the Fallen looks a lot like Mordor.