A lot of things in all EUs are too biased toward Europe. Asians are too weak, Europeans are too strong, Africans portrayed as savages, and American Natives can't fight even smallest detachments from other continents. Chinese base tax should be higher than whole Europe combined, but it would start shouts through these forums. European population didn't explode till late in the game period, and would never be bigger than Chinese. Even Russian population was only twice as big as Japanese.
Back to Africa. Africans were not conquered by Europeans because they were just too strong early on, and disease was indeed a major threat to outsiders (Actually, disease is what made life for conquistadors so easy in Americas, where by lowest estimates half of population died from epidemics). Lack of easy inland transportation didn't help either. Both West and East Africa were quite developed, with strong Muslim upper class due to Indian/Moroccan trade ties. Africa produced mostly resources and would export manufactured and luxury goods from elsewhere. All Muslims knew pretty well North African and Arabian geography, and many East African states had direct or indirect trade contact with both India and China. Firearms were popular and it was one of the few goods Europeans could offer for trade early on. North Africans were a thorn in European underbelly, and quite few naval innovations of the time have roots over there.
But this all is lost on Paradox... I wouldn't expect them to fix any of this in EU4. They ignored it for over 10 years, why do it now? Even if the player start industrial revolution in 17th century Japan or Ethiopia, with Europe falling behind, region will be still considered backward and nothing away from immediate player's reach will be changed. Map of Europe grows all the time, as well as tax values there, while Asia and especially Africa is mostly ignored... Well, at least Divine Wind was made for Far East to try and fix it, albeit it failed miserably.