You came up with a very interesting system with rebels and nations. At its core, for now, this may reflect how empires have affected the world, for eventually some, if not all, of the world will be rooted in a single state. I believe this will work very well with the culture mechanics that will hopefully be added to the simulator soon. Look at this as a cellular automaton, a simulation of microorganisms: stronger colonies capture a petri dish, and after that, all living things in this dish will be related to that very dominant one. You can also borrow some natural processes and the micro world. For example, some microorganisms transfer part of their DNA to others, which can be written into the mechanics of cultures.