I'm get the idea of following the flag colours, and it would work if those colours wouldn't mix up with the background so easily.
Yes, of course you can tell where territories are by numbers, but having territories that are so hard to see makes the map hard to read overall. I mean, you can't grasp the shape of the map with a glance, you have to spend that extra time finding the army numbers, which makes it sort of unfriendly to the players.
Playing the egypt theme with the flag colours is all well and good, but may I remind you of the most important gameplay guideline: function trumps form...
Now you're saying that the army area differentiates just fine... sorry, but I beg to differ here. It has exactly the same saturation, level of focus and tone as the background. If it weren't for the white borders, it would be indistinguishable from the river. Heck, I just now found the Al Gezara territory - earlier I mistook it as part of the background...
The goverment buildings are only slightly better... they get lost in between the houses/buildings, being of the same tone.
Now, there are some options on how to solve this. Firstly, you could make the background darker and the Egypt army territories lighter, so that there would be a clear light/dark contrast between playable/non-playable areas. Or, you could blur out the non-playable area, to raise the playable area into focus... but this would lose a lot of detail and realistic feel of the map... the third option would be to change the Egypt army & Goverment areas so that they would be different shades of yellow and red. You would still be using flag colours, just not all of them...
Well, that's my 2 cents... you're doing a good job with the map, I'm sure you'll figure out a way to improve playability while maintaining a strong thematic consistency.