Underground map for villains (evil heroes)
Create a whole map à la Dungeon Keeper, where villains (evil heroes) can build their cities. This could be an underground instance of the normal map (similar suggestion was there, but more general). There, "pets", "good spirits" etc. should spawn instead of monsters. Create "gradients" where heroes from one side can cross over to the other to fight each other. Make good spirits etc. fight in favour of heroes and monsters fight in favour of villains (but not totally predictable - that's the price of being evil). Make regular attack waves of monsters on good cities and of good spirits on evil cities, so that mayors have to call for rebuilds, expansions and / or purging campaigns.
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rotten.rippchen commented
Ehm, please note that splitting this idea up into parts is a bit difficult, so I posted it all at once. It would be pretty silly to have gradients for map switching or "anti-monsters" that attack villains but no evil map or villains in the first place, right ;-)