This has probably already been suggested but what if some religions chose their religions over tech and degenerated or even rioted until the tech level goes down? or maybe just the tech stayed at the current level.
Another idea is for religions to help dictate the relationships between other empires: if the followers of their religion are fanatical, they might be hateful towards other empires, and those who follow their religion they tend to be friendly to.
And somehow you need to make it so Theocracies tend to exhibit my first idea, because a Theocracy is when religion ties closely into government.