Was the tricolour used by the Tsars? (AFAIK tricolours were a very Revolutionary symbol following the French Revolution) It always strikes me as too modern for one reason or another. Although I must admit my knowledge is a bit limited on this subject. Most games use the yellow with a black dual headed eagle, but that's a bit confusing with the Habsburg flag.
Russia didn't officially have a "national flag" until 1858.
The white-red-blue tricolour was introduced in 1705 by Peter the Great; according to legend it was based on the Dutch flag. However, it was purely a
maritime flag for most of its history, used solely by Russian merchant ships - having Napoleonic army units or cities flying it would be anachronistic. The flag was only authorised for use on land in 1883.
The yellow standard with a black double-headed eagle, displaying the arms of Muscovy (St George and the dragon on a red shield) on its chest, was the Tsar's personal flag. Army regiments from 1727 onwards used a simplified version of this banner with a white background instead of yellow.
In 1803 the design of the army flag was modified to put the eagle on a gold or orange circle surrounded by a wreath, and with four white diagonal rays emerging from it to the corners of the flag: more or less the design Paradox are using here. The colour of the background seems to have varied depending on the region the regiment came from. Bluehawk says that dark blue is for units from the Caucasus; the Flags of the World website says that troops from the Baltic region used pale green.
Russian naval ships used the St Andrew's ensign - white with a blue diagonal cross.
In 1858 Russia adopted the black-yellow-white tricolour as a national flag, in deliberate imitation of Western practices. The yellow and black were taken from the colours of the Tsars' banner; the white stripe was added to make the flag different from the Austrian Habsburg banner. The flag was unpopular and virtually nobody used it, so in 1883 the government allowed people to fly the maritime flag (white-red-blue) on land as an alternative national flag.
tl;dr summary: the flag Paradox has used in the game is the flag that regiments of the Russian army would have carried into battle in 1805. Russia didn't have a national flag then; the Tsars' personal banner (black eagle on yellow) would be the closest match.
