My thoughts on the civs. I have tried to rank them on their longevity, distinctiveness and interactions with other civs. Hope it helps with your choice. I’d be happy to correct mistakes, if you spot any.
Nubians:
Longevity: definitely the longest lasting kingdoms spanning all the middle ages. However, they spent much of that time in a semi-vassal state to the dynasties in Egypt: 6.5/10
Distinctiveness: entirely different from any civ in the game. The Ethiopians definitely draw some inspiration from them as a christian orthodox african civ, though: 9/10
Interactions: spent the entire middle ages only ever interacting with the saracen dynasties up north. Possibly a contact with the Ethiopians: 1.5/10
Average: 5.7/10
Somalis:
Longevity: earliest sultanates appear in the late 9th century and their power only increases through the ages: 6/10
Distinctiveness: definitely influenced by its saracen and Ethiopian neighbours, while preserving a unique culture and language: 7/10
Interactions: often fought the neighbouring ethiopians and came into contact with the saracens. Had a famous alliance with the Ottomans during the Adal-Ethiopian war where they also fought the Portuguese. Had an extensive maritime network reaching as far East as India and the Maldives where they established their own dynasty. Quite impressive for the relatively isolated Africa, but still nowhere near staples like the Mongols: 4/10
Average: 5.7/10
Swahili:
Longevity: first states were established by Arav traders as early as 11th century: 5/10
Distinctiveness: No curent civ even remotely resembles them: 10/10
Interactions: only ever had contact with Arab and Indian ocean traders and a Portuguese maritime mission: 1.5/10
Average: 5.5/10
Zimbabwe:
Longevity: early settlements developed in the 10th century, but were completely abandoned by the 15th: 5.5/10
Distinctiveness: completely distinct: 10/10
Interactions: no contact with other civs whatsoever, only a late Portuguese mission: 0.5/10
Average: 5.3/10
Congo:
Longevity: states started developing as late as 14th century: 2/10
Distinctiveness: completely different from other civs: 10/10
Interactions: nothing to speak of, except late Portuguese missions: 0.5/10
Average: 4.2/10
Benin:
Longevity: first true kingdoms appeared around the 12th century: 3.5/10
Distinctiveness: yet again, 10/10
Interactions: possibly with the Malians: 1/10
Average: 4.8/10
Ghana:
Longevity: the earliest West African empire arose in the Antiquity, but had completely declined by the 12th century: 6.5/10
Distinctiveness: Cultural, linguistic and geographical predecessor of the Malians, but nothing in common with any other current civ, so 6/10
Interactions: definitely with the Malians and according the legends with the berber dynasties as well: 1.5
Average: 4.7/10
Songhai:
Longevity: the kingdom of Gao was established in the 9th century as Ghana started to decline. After a brief conquest by Mali, the Songhai empire overthrew the them and conquered them themselves allowing them to form the largest empire in Africa’s history : 5.5/10
Distinctiveness: fairly distinct, especially linguistically from the Malians, but still share some similarities: 9/10
Interactions: mainly the Malians, who the conquered, and the Berbers: 2.5/10
Average: 5.7/10
Hausa:
Longevity: only started to gain prominence in the 13th century: 3/10
Distinctiveness: fairly distinct from the current civs, though they share similarities with the Malians: 9/10
Interactions: only ever with the malians: 1/10
Average: 4.3/10
Kanem:
Longevity: records point to the kingdoms existance as early as 8th century: 6.5/10
Distinctiveness: share some similarities with the Malians by still fairly distinct culturally and linguistically: 9/10
Interactions: only ever had contacts with the Malians: 1/10
Average: 5.6/10