Overall I personally like this, but Nubian culture should be excluded. While pyramids were built in what we now call Nubia, the people who built them were Cushites like the Somalis or the Beja and predated the Nubian settlement of the region. The so-called "Nubian pyramids" are Nubian by modern geographical standard and little else, whereas the people we call Nubians only showed up after the fact - invited by the Romans (as fellow Christians) to the area in part to pacify the violent Cushitic tribes (ie the Blemmyes) who were, at the time, attacking Roman authority in Egypt and protesting the closure of the last few Egyptian temples. It'd be more accurate for Somalis to do it than the Nubians who threw out the last people to build a pyramid, though the addition of a Beja culture (and additional new pagan religion) would give this a good home and better representation of the region broadly. In lieu of this, following the Berber example (and fetishism in EU4 having the Semitic deity Waaq), African is technically the closest thing - even if Hellenism makes a better fit (eg temple dedications, astrology and astronomy, animal sacrifices) which is why I'm glad you chose to include both.
The Kingdom of Kush in later history, centered around Meroe, built its last pyramids C. 350 CE. While not exactly medieval, it's fairly recent to medieval memory generally speaking, and one might suppose that if such a kingdom rose again instead of continually devolving into angry half-nomadic tribes (that retained their paganism for at least the first 3-4 start dates) then they might hop back onto the trend all over again. Their pyramids were a fair bit smaller, but one might suppose that's a matter of resources rather than intent.
Overall, perhaps not surprising that the Cushites are the people who ran Kush.