Passive faction bonus
I know it has been suggested before, but i still think it would be a good idea to give each faction a natural bonus from the start of the game, that way they are differentiated right from the start. You could even have it so each faction has has two natural bonuses, one positive and one negative base on their lore. They dont have to be super powerfull, just somthing with the same level of effect as having an artifact.