For Guyana and Belize I would leave unless some voices a specific complaint, some colors are going to have to be similar to each other in a scheme so large.
As for minor countries part of me wants to saw "never give up, never surrender!" and leave all the minor countries. However, realistically some should probably be cut. I would, of course, leave any that do have their own color in another scheme. I would cut some of the decolonial constructs such as the individual colors for the Cook Island, Anguilla, Aruba, etc.
Off the top of my head, the only entities I can think of would be the Island of Mann, a color for a unified non-Anglo-Saxon UK, a separate color for different German entities, such as the North German Confederation or a Romance Germany, Communist France or a Blanquist state, I'm sure there are more native nations to add but I'm not familiar enough with them to be able to suggest examples.
Wallonia should keep the color of Belgium. The reasoning, the French speaking Netherlanders are commonly scene as the major cause of the Belgian Revolution, ergo the French speaking region keeps the color.
For Hungry, Malaysia, and Burkina Faso see the comment on Guyana and Belize.
For Greece a color for Mycenae for any really early timelines might be nice, the only other I can think of would possibly be Corinth. Separating Athens and the Byzantine I think would be a good idea. Lastly, I would as a note about using an outline of existing colors for things such as the Delian league and Peloponnesian league.
For South Africa I would say defiantly separate Zulu and Lesotho, a separate color for Xhosa sound good to me.
As for Japan see comments on Hungry, Malaysia, Burkina Faso, Guyana, and Belize.
As side note something I would do is combined the religion colors to the country whose color they share so that they are still there but you don't need the separate category. Also I think a good idea would be do the same thing with governmental systems, such as representative democracy, constitutional monarchy, absolute monarchy, elective theocracy etc.