I have a few suggestions for factors that might have played a part.
Firstly, I should disclaim that I am obviously generalizing. This thread might be better off talking about specific regions instead of the continent as a whole, but it's not doing that, so I'll generalize.
Firstly, I think Africa is relatively lacking in waterways. Europe and China are criss-crossed with giantically long rivers, as is North India. Europe has enormous amounts of coastline for its size, and places like the Arabian/Persian gulf and Mediterranean Sea were hugely important to early and later civilizations - as is the Nile, which is African, of course.
Also, I believe there are many parts of tropical Africa where rivers were pretty heavily infested with bugs and parasites, which would disincentivise settling near them (or traveling on them).
I would suppose that tropical or sub-tropical climes tend to encourage the evolution of nasty bugs and parasites, but I am not sure I have a scientific rationale for thinking so... I would think it isn't blind luck that North America and Europe don't seem to have many... Denmark's most deadly animal is the bee (and our bees are very docile). I would guess that tropical areas simply create very bacteria-friendly freshwater bodies, which promotes the spread of viruses (which eat bacteria) and cause otherwise harmless bugs to be extremely dangerous disease vectors. Whereas in the North, the growth rate for bacterias are lower, which aids the growth of freshwater plants and algae, which in turn creates food for animals instead of diseases to be vectored.
The Nile and Mediterranean are famously easily navigable waters, to my knowledge, and the Baltic and North seas are not much harder. This encourages trade and the exchange of ideas, like the Silk Road, but several times faster.
My understanding is that historical African nations were relatively well-developed on the coasts, but were always subject to mass migrations from inland areas, which supported enourmous populations. This could cause destabilization in regions that were well on their way to becoming well-connected trade empires, but had much too little manpower. This is not unusual, though. The Dark Ages could be described in similar terms (Massive numbers of North, East, and Central European tribesmen migrating West, eventually taking over Gaul and Italy).
Another problem for the African nations that were seafaring is that it takes them longer to reach anything. It's hard to link up with Indian and European trade routes if you're on the other side of a continent. And even if you're in the East African region, the Arab and Indian trade routes are still farther away. If you're in Mali, your trade outside of East Africa is still controlled by North African Muslim states and European heathens. And Brazil wasn't that interesting at the time.
Also, there's an extent to which modernity can really only happen once. If you're *almost* ready to start building a major empire with massive warfleets with cannons, but the British get to you before you do, what happens? They can bombard your cities and shipyards from a range you can't even reach. I think the "race" to global supremacy was always going to be won by whoever could field a large navy capable of reaching halfway across the world. Because at that point, Britain could win any war with any smaller or less technologically advanced nation, and then use that victory as a way to leverage more power and expansion. In other words, it's a snowball effect. So African nations might've been nearly as advanced as most anyone else, but their development was immediately halted when British gunboats started blowing up forts over trade disputes and minor diplomatic insults.
In other words, the great empire was always going to go to whoever got into the position of taking it first, which is why Queen Elizabeth II (yes, the one who still lives) has been the queen of Kenya, Uganda, South Africa, Austrialia, India and Pakistan (Including Bangladesh, "East Pakistan").
Which means that the native technological or social development of Africa might've actually done a reasonable job keeping pace with that of Europe, but was immediately halted because they didn't reach the goalpost first. In other words, our image of Africans as being developmentally "behind" is not caused by Africa being much slower to develop - Rather, they were *a little* slower to develop, and then the British won the race, was awarded a large cannon, shot the other runners in the legs, and kept going.
Not to say that colonialism caused every problem. But if you had had a thousand ships off the coast of the British Isles in 1550 crewed by the Malinese Royal Navy, the world would look rather different today.