Neat read, but I would also consider the Han -> Mongol -> Qing stack to be a valid China stack given the Mongols would just represent the Yuan dynasty in this case.
Your Aksum stacks are weird, obviously none make a coherent civ, if you want a coherent three prong path you would go Aksum, Zagwe, then Ethiopia. (Or Ethiopia -> Ethiopian Empire)
For a West Africa stack I would go Ghana -> Songhai -> Sokoto, and for Buganda, I would do Aksum -> Kitara -> Buganda. Can also have a Zanzibar in the Exploration age and a Oman Sultanate in the Exploration age if they want to represent the Swahili.
Southern Africa just lacks an antiquity civ full stop. But they can do Mapungubwe in the Exploration age and Zulu in the Modern Age.
Prussia stack makes sense, obviously the middle stage would be the Holy Roman Empire, question is what would be the Ancient Germans? I could see it being the Franks (To fit Charlemagne), the Saxons (To allow for growth into England, Scandinavia, or Germany), or the Goths if they really just want to counter Rome.
If they had a Saxons, it would work well to then go into Denmark, then Sweden for a Scandinavian line. Saxons could also go Saxons into Normans/English into Great Britain. Having a Celtic civ in the ancient era is also cool, Whether its the Britons or the Gauls.
I understand the appeal of having the Celts be a macro family civ that can encompass the Gauls and the Britons, but that has been unpopular in every instance it was tried. I really think they need to commit to either the Britons or the Gauls. If they pick the Franks they could do the Britons, if they pick the Saxons they could do the Gauls.
Rome is a fine precursor to the French stack, but I think any variation of these works Rome / Gauls / Franks -> French / Normans -> French Empire
Arabia is difficult, we have the Abbasids, but I don't know that there is a good pre-Islamic pick other than just Egypt. The most reasonable options for me all start with Egypt, but into the Abbasids, then there is a lot of modern options: Saudi Arabia or Hejaz, Mamluks, or Ottomans. All of which make the most sense for that region.
Assyria can't really have a line, since its people don't really have a state into the medieval or modern age, but it can easily transition into the Persians or the Arab states.
I don't have a strong opinion on a precursor to the Inca, because there is a few cultures that could be covered by they are all small. I definitely want a Peru though. Gran Colombia will probably come at some point, but it isn't Peru exactly. It may just have to be good enough though.
Vietnam should not be grouped in a Southeast Asia stack. Vietnam is of a very different cultural group and it irks me to no end when people treat Vietnam as though its somehow deeply related to the Khmer / Thai which are of a totally different culture.
A Southeast Asia stack, which I would call a Pallava stack (because they all use Pallava based scripts) would be Khmer -> Ayutthaya -> Siam or if they want to be spicy, do Khmer -> Pagan -> Siam
Vietnam stack would be Han China -> Dai Viet -> Viet Nam, if they really wanted to be fancy they could do Nanyue or Au Lac, but its not really necessary. Just having the Han Dynasty be the start is fine.
The India stack is fine, but I am happy we are getting Nepal so we have some options.
Maya -> Aztec -> Mexico is also fine to me, as is the Mississippians -> Shawnee -> Americans as valid stacks.
Naturally they have their alternate paths as Rome -> Spain -> Mexico and Britons / Saxons / Romans -> Normans/English -> Americans.
Unfortunately as much as I would love the Sassanids, I think the Seljuks are the only really likely Medieval pick for the Persians. Persians -> Seljuks -> Qajar. It also makes an easy path for Turkey.
Turkish stack would be Xiongnu -> Seljuks -> Ottomans, and the Xiongnu would also make for a good Steppes / Mongols Stack which would be Xiongnu -> Mongols -> Qing. I would not consider the Xiongnu -> Mongols -> Ottomans to be a "Mongols" stack.
Rome -> Naples / Venice -> Italy would be a good stack, Sicily also works, but is a much more limited time frame than Naples.
Heian Japan is a good precursor to Meiji Japan. Yamatai would probably be the Precursor to Heian Japan. Silla isn't technically correct. Gaya would be the closest relative on the Korean peninsula that we know of, but we know a name for an ancient Japanese Kingdom (Yamatai) and its related to Himiko, So its fine to use.
Korea obviously goes Silla -> Goryeo -> Joseon. In theory they could evolve Silla -> Mongols -> Joseon much like the Chinese can do Han -> Yuan -> Qing. Both would be valid.
Last few stacks i can think of that were not expanded upon too much: Greece/Rome -> Byzantines -> Russia/Ottomans would be either an Roman Orthodox Stack or an Anatolian Stack.
As well as all the various Slav stacks which seem to have been forgotten in your list: An ancient era Slav state is pretty dang difficult to think of though. I would generally just recommend we start with the Huns/Goths then that can evolve into either Poland or Kievan Rus, then into Poland-Lithuania or Russia.
If you have the Huns you have an excuse for Hungary as well. Although we may actually have a relatively decent line going from Greece -> Bulgaria -> Russia, even if it misses an important step, it does create a logical line to transition from Greece to a Slavic state, then to Russia.
Anywho thats all my spitballing. Glad to see other people interested in making logical paths as well.