Well, I actually have two suggestions.
One of them (inspired by the skyrim Dwemer plot) is that the gods have actually disappeared, but they have left there marks in the world ...maybe some temples, some signs of their former existence ... However, here you get to do what you failed in Skyrim - you get to bring them back ... Search them, activate some mystic altars and perform some rituals, sacrifice a lamb or two, do whatever it takes to restore some of the old glory to the benefit of some races - or the doom of others. Would be some rich plot options in this.
Another suggestions I like a lot as well is that Gods exist, but nobody is so sure of that, because they have gone into hiding - as "normal" people. So basically everyone and everybody you meet could be a god, and it depends on your actions during the game if they reveal themselves to you or not. Adds some effect of surprise and consequence.
Let me know if you think those are any good, would love to discuss continuous plots/storylines for those two ideas.
"And may a projective EternitY be with you."