First of all, I am glad that Ageod did introduce Stars & Bars in 1.01. It's much more realistic this way. I now hope the Battle flag will take its place on units and replace what's left of the 3rd national elsewhere.
A suggestion, though: individual states do have flags too now. Confederate ones often had old pre-war design that changed after reconstruction or switched upon secession, whereas in game flags are the modern ones.
Here is a link with the confederate version of the separatist states.
http://en.wikipedia.org/wiki/Confederate_States_of_America#States_and_flags
It would be great if some were introduced.