I agree...the coloring is one of the few areas i didn't like about it. It makes it very hard to tell who is who. I like the idea of similar colors for the common wealth, but i also think it makes things a lot harder to figure out once the action starts.
When the Soviets DOW Japan i thought the lines didn't move, but when i clicked on Korea to bring up my intel- it was Soviet controlled. ...really confusing.