I think what they really need to add is some kind of colonization difficulty rating for different provinces, sort of like in Victoria 2, so that it is always more profitable for Europeans to colonize somewhere else. Of course, that then leads to WC problems and other things. Maybe a different colonization system for Africa, like CNs for America and trade companies (which would become Asia only) where you instead just make small trade posts along the coast and trade with local kingdoms for slaves and things, with no real reason to expand inland?
Also, how would the inland nations interact with the rest of the world? If they are literally completely separate, they probably shouldn't really be bothered with, as they would just be their own thing. Was there any outside contact at the time, at least indirectly through coastal kingdoms?