The combination of the two gods used in each game creates a unique texture to that session. They affect draft choices and influence the flow of the battles. Will you try to benefit from a god's power again and again by moving them where you want and always pillaging their province? Or will you do your best to neutralize them by pillaging around their province? Perhaps you'll want to attempt a hopeless pillage on their province just to move them onto another province where they will hinder another player's plans.
They add a whole new layer to the game, without adding hardly any complexity to the rules.