because Africa was extremely primitive during the middle ages

On the contrary, the Mali Empire existed in the 14th century, and was extremely powerful. Africa had a number of kingdoms and empires that rose and fell before, during, and after the middle ages-- these kingdoms were wealthy, administratively complex, and had complex trade networks within and beyond Africa. It's just that details about them are less known, and even less taught. Most of us grow up with a very eurocentric history. Colonization absolutely destroyed Africa because a bunch of European powers chopped it up and drew borders that had no bearing on ethnic or linguistic lines, imposed European laws and values (and religion), and heavily exploited Africa for material resources and slaves. The core pillars of society-- the social network and glue humans rely on-- was severely disrupted.

As for China, another part of your question was already answered in this comment thread here. It has nothing to do with intelligence and everything to do with the fact that China had increasingly regressive and conservative policies. The Ming and Qing dynasties were really struggling to retain power over a territory that was really just too large to manage effectively, which could not sustain the number of people it had, and was not enacting effective policies or solutions to problems. The Chinese Imperial system was slow to change and fairly xenophobic, and the emperors at this time were what I'd call extremely out of touch. These were not men who demonstrated the ability to enact practical solutions or good problem-solving skills, not by any fault of natural intellectual ability, but because the education emperors were given at this time simply did not prepare them for this. They were taught the classics and Confucian philosophy, not how irrigation systems worked.

If you look at Japan, you'll notice Japan went through a period of rapid industrialization after the Perry Expedition in the 19th century, and rose to power very rapidly, and is a very successful country today-- even despite what happened to it during WWII and the aftermath. Japan had a lot of things that made its rapid modernization possible which China did not (for example: being a much smaller country), but at the same time, Japan also demonstrated a willingness to adapt that China did not... greatly helped by the fact that the Tokugawa Shogunate was overthrown in the 19th century, and Japan adopted a european-style Cabinet system. Things like public education and the abolishment of the Samurai class were changes Japan made that contributed to its successful modernization.

Northern European countries were far from "stable" during the middle ages. They were constantly at war with each other. States rose and fell in power and were unified or absorbed over time (for example-- many cities in Italy today were once independent city-states that competed economically and warred). The Crusades of the middle ages did not come about because Europe was an amazingly stable place-- in fact, quite the opposite. Europe had a lot going for it, don't get me wrong, but until the Renaissance, it really did not have a leg-up on its international contemporaries. And due to their close contact with each other, they were in a kind of arms race that China and Japan did not have. Japan invaded Korea only a handful of times and only ever had to defend its borders twice (both times against the Mongols) prior to the 20th century. China fought a number of wars. But Europeans fought hundreds of wars and skirmishes with each other, eventually had the democratizing effect of the printing press, and were in constant competition with each other over things like dominating the sea-routes or controlling the seat of the Pope or the Holy Roman Emperor. Civil wars and revolutions abounded. "Stability" was an illusion.