But, I really think a couple of independent/native cities should be added. For example, with Quelimane and Zimbabwe, I think Sofala should be there. It was an important trading post of the eastern African coast. Also an independent or barbarian Turku should appear in Finland at around 1100 if no culture is overlapping it's tile. If the vikings conquer it, it should rename to Åbo.
Regarding eastern Africa, I think the Arabs should show some interest on the cities on the east coast. It's true, they never conquered them, but most of the east coast of Africa is Muslim, and since this is a mod with the chance of an alternative history, I just think it could be considered reasonable. This way Islam also could spread easier to the African east coast.
Also, the jungle-tile in Ceylon should be converted to grassland or the spices should be added on it so someone might have a chance of building a city there, before needing to research biology.
And finally, I have mentioned this before, but I really think that slaves should be added as a resource, since slave trade has been the biggest form of trade through history.