When I play, the same thing basically happens to the nations.
Some civilizations played by the AI do really terribly, and some do extremely well.
Some ones that do poorly are Moscow, Austria, Hungary, and Sweden. Austria always becomes vassalized only owning Wien, Prag, and Kopisch or Klagenfurt or Grosskirchen. This is annoying since they, in real life, became a powerful state. Burgundy also becomes vassalized by Frankia, which is fine but I think they should just be taken over. Turkey rarely takes over Instanbul by 1500 in my games. I've never seen Cordoba been defeated, which is

.
Frankia, Arabia, Spain, and sometimes Venezia become very powerful.
Also, should Bysantium really be that unstable all the time? They never ever really hold onto the seven cities of Iconium, Caesarea, Antioch, Sinope, Aleppo, Alexandria, and Cyrene because of them declaring independence... I probably wouldn't know, but I don't think the Bysantines would declare independence from the mightiest city in the world (Constantinopolis) and its empire.
Some more of my problems were as Sweden, my last UHV never got checked (which I would have one) and neither did my last UHV on Venice.
As Bysantium, I lost my last UHV (have the most gold in 1500 A.D.). Somehow someone had over 6,000 gold? Is research python-based? Sheesh, how do they have that much gold and still have average techs? If they had low techs surely they would have been taken over...
One last thing: when I take over someone, they might rebel, even though my empire is "Stable" (in the financial advisor window).