Haven't engaged much with this thread, but I think that the majority of posters have missed the point: I don't have a problem with natives rising up in uncolonized provinces, and I know that these natives get relatively weaker over time.
The issue I have with the current game state is that the natives are much stronger than the African nations at the game start (especially the non-feudal ones) and for a long time after, owing to every uncolonized province in central africa having high bonuses to tactics and morale. Other posters in this thread have also highlighted that all natives are considered one entity and they gain army tradition over time which gives them even more bonuses. I did hear about this in the past as well, and I think it is also a problem, but it isn't the case here (the time in-game was 1445 in the screenshot).
The reason I mentioned in the OP that I lost 2000 troops to these natives compared to 850 from the nation of Busoga, was to highlight that these natives deal 2.5x more casualties compared to the bordering nation of the province. The reason this was astounding to me and prompted me to make this post was the fact that I had a very strong army, with 112.5% discipline (strict ruler + discipline advisor + mwari cult) and 25% bonus morale (for reference, the starting morale as Buganda is 2.06, in the screenshot I had 2.5, owing to temporary army morale bonus mission, AT, prestige, and PP), and that I still wouldn't be able to beat a few provinces of natives. Of course, these numbers aren't perfect and they would likely be better tested in a calculator, but I doubt they'd be all that different, because the natives do have demonstrably better stats.
I disagree with the preposition that the imbalanced power of the natives compared to starting nations is intended, owing to the fact that gameplay surrounding uncolonized provinces is a complete mess, with AI nations shatter retreating all the way to Narnia through these provinces whenever you defeat them in battle, and the fact that supply lines in general are a non-feature of this game, making the argument that this
of all places is where it ties in, a bizarre one.
Just so that this isn't just an essay, I decided to record a 1-minute video showcasing how gameplay looks in Africa, take a look ;D : https://files.catbox.moe/zbna73.mp4
And perhaps for a bit of comedic effect, this is the rest of the recording: https://files.catbox.moe/gevdz0.mp4