We can work these issues, I believe. While it will never be perfectly balanced it can be improved on.
As a point of reference, the City for each country is represented in a geographical location. The Red City is located generally where London would be, the Green City is located generally where Berlin would be, and the Blue City is located generally where Rome would be. I believe these need to stay as they are.
The other Strat facilities can be moved as needed to balance the accessibility.
I think one of the strong points of this map, is the uniqueness of each country. No two are the exactly the same. Each has strong points and weak points, very much like the ETO was in WW2.