Rage Against the Heavens
As is possible to find Demons if digging long enough, there could also be sky layers where the Gods themselves or possible celestial entities thrive. There should be possible to get into the layers by climbing the highest mountains(if existent), building a Babel Tower, or somehow through a portal.
Variations
Ubercivilizations: Heaven/Hell could be civilizations just like the others, but in dormant war against each other, just waiting the right conditions for unleashing a Apocalipse/Ragnarok.
Hell and Heaven for Real: Souls of deceased sentient beings should go to Heaven or Hell: almost everyone to Hell, and some lucky ones to Heaven/a lesser worse part of Hell.
Holy Quest: In a even more extreme variation: your race is in a quest to save the world by preventing the triggering of Ragnarok. Ragnarok happens when Heaven gets enough warriors to fight Hell(enough soldiers of any race dying in wars, specially holy ones). When Ragnarok starts, Heaven starts a preemptive strike against Hell that potentially lays half the inhabited world in a wasteland where even undead don´t thrive. The player can prevent that souls go both to Heaven or Hell by dispatching them through special Void Pits, were they can turn in valuable Aether, or Dark Matter. Souls could both be snatched inside them, rightly robbed from Heaven or Hell, or convinced on going them through proselitism. The number of souls sent into the Void maybe should cause, however, the awakening of other forces...
Golam Wing
Civs make use of mountable mega-beasts operated by special people known as pilots. They use these beasts in their wars against each other.
Variations
Golamgelion You has a collection of beasts and pilots, and a extraordinarily well-built fortress, but also are attacked by a consistent collection of Angels who try to lay wast to your base.
Rise of the Machine-People
There are another Civilization, which lives in sites know as Assembly Lines. They want to purge the world from all impurity. For them, the most impure are the undead, hybrid creatures and other great creatures, which they hunt actively. After that, they want to purge the very source of evil: sentient creatures who generate the undead and mutants, either by destroying them, or reassembling them as machine people also. Is rumoured that the Machine-People are controlled by a Great Technician who has the codes which made machines controllable.
Variants
Technowar: Machine-People exists, but no such Machine Civilization. In place of that, there are various Technolords who demand that people give Raw Power or aethricity to them, so that they can fight their competitors. The Technolords Spires cause great enviromental destruction around where are, causing even the undead to flee them. Within time, any place around their influence is rendered a grey area full of pollution, espefically aether radiation.