The one god per town in EB1 was a hold-over from vanilla. After all the work that went into traits and ancillaries that deal with indivual gods, it would be hard to rework the entire temple system. But since EB2 requires the whole system to be reworked anyways, it will be reworked differently then EB1. And remember that M2TW temples work differently than RTW temples, with each religion having only one choice of temple, which vanishes when another religion conquers the town.
I've thought about making a minimod that changes temples in EB1 so that each culture has its own temple with overlap in cultures that would assimilate other's gods. Like one temple complex for Hellenic/Roman/Phoenician/Egyptian gods, one complex for Zoroastrianism, one complex for Gallic/Iberian/Germanic gods, and one for steppe religion. But the complexity of the traits and ancillaries has scared me off.
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