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actually before Peter the Great there were quite a few flags in use, red ones with the eagle, green ones with the eagle, yellow ones with the eagle, white ones, blue ones...

I just figured Paradox knew something I didn't and went with green ;)
 
Not quite. Or, Paradox knows something I don't, that is, living in Russia. I have NEVER in my life seen a green flag of Russia - never in the museums or anywhere else. So, I think it just went along with green uniforms :)
BTW, the early uniforms must be red (streltsy during Ivan III - Ivan IV's rule), and during Peter's reign only Pawlow regiment had green uniform (though we never had a national color).
I find yellow shield closest to reality. Now we have a red one. Blue was used several times, but, I think, it was reserved for special cases. Never seen green or white.