The historical timeline serves as a guide for scenario makers to make realistic borders with countries. Since this map has so many territories in specific areas, people can be confused as to where the borders are. I'll have those bonuses set to 0.
As for not having individual bonuses for each territory, the problem arises that certain areas may not have much of an importance compared to others. Here's an example:
You can see that Paris is way more developed than its surrounding countryside. If Paris and the countryside were made into 1 bonus, however, I will have to find the mean value of all of those territories, undermining the territory value of Paris, and increasing the territory value of the countryside.
Geopolitical regions also reflect the ambitions that a nation has to conquer a specific region. For example, it could be Schwyz's ambition to conquer all of Switzerland (Schwyz was a tiny state that over time grew until it covered all of Switzerland). Same goes with Prussia and Germany, or France and uniting all of France.
If I were have to choose 2 out of those 3, I would choose including the historical timeline and the individual bonuses. I feel like people can understand enough as to know which region they want to conquer.
Lastly, as for the colors, the range of the importance between one territory and another is vast, so I would need many colors for that to work, which will be confusing.
I think what I'll have to resort to doing is to combine multiple territories into one, which will undermine the historical accuracy of the map, but will increase the playability of it. I don't see any other solution.