The scramble happens because they are ahistorically weak, but nations who devoted resources to conquest did succeed like Portugal in Zenj.
To make Africa historical you have to include the effects of disease as someone mentioned, but you also need to fix the fact that the scale is off. I estimate there should be 4x as many provinces in Africa as there are (mostly very poor). That's why, for example, it's easy to colonize the whole of modern South Africa in EU, while historically it was most of the way through the Victoria period before that colonization process encompassed South Africa's modern borders.
As a bonus, 4x as many provinces would make the native kingdoms much more interesting to play. West Africa should look like the HRE.
On another note, Paradox mentioned somewhere that they wanted to include trade posts in vanilla EU IV but decided they didn't have time. I think it's likely that there will be a DLC both adding trade posts and improving Africa.
(Actually, there should be about 4x as many provinces throughout the world outside Europe and Japan, but that's another thread.)