The scramble happens because they are ahistorically weak, but nations who devoted resources to conquest did succeed like Portugal in Zenj.
No. Their weakness isn't ahistorical, although the ability of other nations to project large forces long distances is. But Africa wasn't colonised in force until past 1800, because disease would devastate any garrisons, making rulership effectively impossible (as an aside, this would also be a problem for any pan-african empire). Its not a problem that could be fixed with any technology existing within the EU period.
Of course, 'you can't do this, your men will simply drop dead' isnt a message players want to hear - that said, I'm not sure 1500 African empires are something I want to see every game.
Even that wouldn't matter so much - players will want to kill off most of the African states just for the sake of streamlining their trade routes. I think we need to bring in some nasty attrition modifiers for tropical provinces to give an idea of how inhospitable these places were to outsiders (and even locals to some extent) due to diseases like malaria and sleeping sickness.
That is also true, unless Paradox bites the bullet and rejigs trade to cut them out (either making inland nodes to cut out inland provinces, or lets people bypass them entirely).