I dunno, i'm getting too many mixed ideas about the bonuses, so I took your recommendations and compared each territory with popular maps in existance and have come up with this. I think its good and the map is about done.
Athens - 6
8 Countries, 4 borders. Took your advice for it.
Sterea Ellada - 3
5 Countries, 3 borders. Reminds me quite a bit of classic Africa, which has 6 countries and 3 borders, and a bonus of 3.
Peloponesos - 5
8 Countries, 3 borders. Reminds me a lot of Classic North America, which has 9 countries and 3 borders and a bonus of 5.
Asia Minor - 5
9 Countries, 3 borders. Pretty much the same as Peloponesos with one more country.
Borea Ellada - 3
7 Countries, 2 borders. A lot like the European Near East, which is 6 and 2 and worth 3 bonus points.
The Agean - 2
4 countries, 2 borders. Reminds me of Classic South America as well as the European Western Russia, which are both 4 and 2, and both have a bonus of 2.
I realize a lot of the bonuses are similar, but I kind of like that. Could make for games with a bigger buildup.