We can create some very interesting historical paths throughout Africa. Here are some suggestions of mine. Obviously, I'm not convinced that we have enough materials to make all of them playable civs.
1. Maghreb
Numidians > Marinid/Almohad > Morocco
Personally, I have a slightly stronger preference for Marinid, but Almohad would also work quite well. By the way, I love this path and hope to have something similar at some point in the game.
2. Sahara Desert
Garamantes > Songhai > Kaabu
I'd like to point out here that I'd have preferred them to have gone to Mali instead of Songhai, and I don't think we'll have both included.
3. Akan States
Bonoman > Denkyira > Ashanti
While Ashanti and Denkyira fit well into their Ages, Bonoman is way outside of what Age 1 would be.
4. Nigeria
Ife > Benin > Oyo
Ife is way outside of what Age 1 would be and I can't think of any other option.
5. Ethiopia
Aksum > Zagwe > Ethiopia
I think this path works quite well. We could expand this path and call it the "Horn of Africa path" and put Somali (or more specifically a Sultanate, like Ajuran) in Age 2 instead of Zagwe (or could we create a Somali path of its own?). I'd be fine if Nubia was also part of this path as Age 1.
6. Southwest Africa
???? > Ndongo > Kongo
The transition from Ndongo to Kongo works well, but I can't think of any options for Age 1.
7. South Africa
Mapungubwe > Mutapa > Rozvi and Zulu
Mutapa was very prominent in the region, so I chose it over Zimbabwe (I'd be fine if Great Zimbabwe was a Mutapa-associated wonder). The transition to Age 3 could lead to either Rozvi or Zulu, depending on the player's choice.
8. Southeast Africa
Swahili > Kilwa > Omani and Buganda (???)
This seems like a good historical path to me, but I'm not sure there are enough materials to make an Age 1 Swahili civ. Perhaps Buganda could function as an alternative successor to Kilwa?
9. Madagascar
Vazimba > Merina > Madagascar
I'm pretty sure that Age 1 of this path is too obscure to be a viable civ. Merina, however, is pretty easy to make a playable civ because it's well documented.