My current thoughts for the feature are: a pantheon of 5 or so gods and godesses, each with a different area of interest. The player can build temples to curry favor with the gods. The more favor with the god, the more benefit the god gives. The player can also invoke the god for miracles.
As an example: Akkan the Skyfather is the god of the skies, and father of the pantheon. Earning favor with him provides favorable weather (occasional light rains, fewer storms). He can be asked to create a storm, with lighting bolts striking enemies.