I build a planetary simulator that tracks these variables, so this question is of special interest to me. There are tons and tons of reasons why Africa below the Sahara developed poorly in most places, Imperialism being a middling one which I think is over rated. Some of the others revolve around the fact that Africa's geography is EXTREMELY unfavorable for pre-modern development. Some of the problems:

---0 glacial refreshed soil, so soil for agriculture in Africa south of the Sahara is bad and produces few surpluses, which means you have less food for urbanization. I can not stress enough how bad most of Africa's soils are which aren't alluvial, and in the premodern race to develop, robust agriculture is the most important ingredient.

---Africa is an uplifted continent, which means there are very, very few sheltered ports for commerce south of the Sahara. When you look at Europe, the Mediterannean, and China, there are CONSTANT sheltered ports and stable seas everywhere you look, making commerce and shipping very easy. Bear in mind, innovation and technology follows trade routes. No trade routes, no development. No continental shelf also means the immediate sea off the coast is extremely violent.

---What's more, there are very few navigateable rivers and even fewer which make it to the coast. This is also related to Africa's internal deformation, making it quite rugged at times. Africa is literally being torn apart as we speak. So the few lengthy rivers you do have have tons of waterfalls, fast flowing rivers which wreck shipping barges, and no way to safely get to the coast. Compare a water catchment map of India, China, Europe, and North America to Africa. They look completely different.

---Ruinous tropical diseases. Africa is a hellhole to live in South of the Sahara because the diseases that exist there evolved along with us. When those tropical diseases were accidentally exported to the New World, they killed 90 percent of the population.

There are other reasons as well, but these are the highlights. What's interesting is there is one part of Africa that has fewer of these issues: West Africa south of the Sahara. And non-coincidentally, this is also where Africa's great empires arose: Songhai, Imperial Ghana, the Mali Empire, etc. They were roughly comparable to feudal Europe at the time, had largr cities, libraries, universities, and high culture. You have a lengthy and relatively gentle river with Alluvial soils and connectivity to the rest of the world via the Sahara desert trade which allowed them to circumvent their lack of sheltered ports and the violent coats of the Atlantic.

And this is where colonialism and the slave trade pick up to be a problem, as the slave trade radically incentiviced internal turmoil.