Since American colonization got improved via DLC, perhaps a second colonization DLC could fix Africa and Asia colonization? I'd buy that.
It would have to overhaul the gameplay on Africa entirely though. It should introduce tradeposts for the Europeans perhaps coupled with the Protectorate system already seen in the Live Streams? It on the other hand shouldn't exclude the native kingdoms like Mali or Songhai to expand their borders inland.
Would it be to far fetched to suggest an Africa which is open to the natives yet closed to the outsiders - whether European or Muslim or Asian, the only ever attempted expansion was that of the Moroccans which ended in a sad deluge at Timbuktu, the price of communications across the Sahara (also an abhorrent feature of the map => there were multiple routs across the Sahara dessert both from Morroco and Algiers - see the maps in Braudel's Mediterranean - yet they choose to display it as an arbitrary north-south route that looks so ugly on the map).
Native 'African' culture/Tech Group should be allowed to colonise an extended interior of Africa - with features along the lines of what the natives of the Americas will now receive, but then geared for the African context. In terms of taxation the majority of these lands would be piss poor, but it could in return be migitated by wealthy trade. This trade would thus be in luxury merchandise such as ivory but also in humans of course. May not be nice, but the major feature of African trade was the slave trade both with the muslim world and with the Europeans - both distinctly different in nature, thus leading to different events as well. A muslim nation with a strong share in the African slave trade should get events like 'the most beautiful servants' or 'lazy servants' or whatnot while Europeans should get events related to the harsh exploitation of slave labour proper, 'slaves revolt', 'slaves runaway', etc.
European slave trade was the harsher of the 2, geared for forced labour in abysmal conditions across the Atlantic, muslim slave trade was geared for domestic household slaves and women, not labour (the only time the a muslim state relied on slave labour proper was the Zanj in Abassid Iraq - ended in full scale revolts all over the place). European slave trade was highly disruptive, taking hostage the native socio-economical and politico-institutional development. Henceforth the west African states were no longer their own masters, but were defined by their approach to the Atlantic triangular trade: either deal with the Europeans and receive arms and whatever trinkets or try to resist them, which meant generally fleeing landinward and building up a state there. In game terms those that choose the former should get military bonuses representing European arms while those who choose the latter should get other bonuses indicating their resistance (could be morale, or in terms of manpower/prestige/taxes/etc).
European presence in the main time should be focused exclusively on the litorral in Trade Posts. These should be a miriad of small colonisable provinces (or an other option 'trade post' in this context) which would serve as focal points of your presence in Africa and your progress beyond, sailing for the Indies or whatnot. The Europeans could install protectorates over certain states, either by diplomacy or manu militari, for example over your 'favoured' supplier of slaves, but just as easily over the non-slave trade geared nations mentioned above.
European (or Muslim, Asian, etc) colonisation of the interior should be excluded wholesale as it was simply IMPOSSIBLE. People died. Horribly. Conquest of the already existing native states should be either impossible or restricted to the coastal area in some way, control over inland regions at best should work through a system of protectorates. It should be possible to say capture Mozambique or Congo, but the cost should be tremendous in multiple ways and thus in reality something rather not to pursue, thus directing you towards a more subtle approach. Say I'm an ambitious Portugal and I seize manu militari the Congolese seaboard, there should be an option compared to the 'liberty feeling' of the new DLC but in terms of 'native tensions rising', when it boils over - which if you are only pursuing a 'gain' strategy (get money, get trade etc) it should - leads to full scale revolts. The possible alternative would be to extremely placate the locals at a high cost (ducats etc) while losing prestige at home (you silly Portuguese handing money to African tribesmen...).
But, you may say, full scale revolts are easily crushed by European troops, Africa's tech level does not allow any form of military resistance to the European mighty arms! Correct I say, thus this should be mended in other ways. I'm thinking of expanding on what has already been mentioned: remember how you now destroy Mali with 5000 infantry? Wrong, guess again! 5000 European infantrymen marching into the African interior does not equal ??? does not equal profit... It equals DEATH EVERYWHERE
What Africa lacks in military strenght it should make up 2-fold:
1) Large (rebel) armies. Yes, here we have to be somewhat liberal. It isn't because the Zulu's of the 19th century could mobilise over 20 000 footsoldiers in their impi's that all 16th century African states should be able to, but will omit that for fun's sake.
2) Enormous negative modifiers to European (and other) armies making landfall in Africa. Land forcelimits should be minimal, attrition devastating. Any army larger than say 1000-2000-3000 men should literally melt away. Especially moving away from the coast should incur serious negative bonuses in terms of morale etc (simulating the devastation wroughty by sickness), making cocky European invaders easy prey to the numerically larger yet technologically inferior African armies. The coast should thus be a feasible hold out but nevertheless to costly.
The player/AI should thus be steered in a more diplomatical divide and conquer approah to Africa. The Trade Posts should allow for larger armies to concentrate but not by much (say 4000-5000 mn), they are after all transit zones. In intra-African tribal wars European 'protectors' could be called in as well. You could then attach a force to a native army to support your candidate for victory. Same rules still apply: anything over 1000-2000 should simply melt away. What I'm thinking of is that by attaching a few regiments, even 1, to a native host, you should be able to somewhat influence the outcome of battles, still the cost should be hard in terms of manpower, and adding to many troops should have the reverse effect of seriously lowering the morale and thus spell certain doom for your combined force. There could perhaps be a modifier that seriously increases your exhaustion when having a certain number of troops fight on African soil.
The exception to the rule should be Southern Africa, at least a well specified region of it, this should be open to colonisation as it was. It was the only part of Africa the European settlers discovered to be climatologically benevolent towards the European lifestyle and agriculture. This region would allow for colonisation proper (why not in the future a colonial Cape Colony-nation?) and also have higher force limits making for bigger armies to be stationed here. Europeans should be eager to fight over this transit zone towards the Indies.
I started out thinking 'keep it short' but it ended somewhat like this. Thoughts?