I took drawings of ACW flags and then scaled them down for 6mm, and learned a few things:
Union national flags all look the same, even if the star pattern is different or they have a bit of writing in the stripes, you cannot tell. You can tell if the red stripe is not on the top – that stands out.
The blue Union regimental flags all look the same.
There is variation in a few of the Irish Union flags.
You can tell the different symbols on the Union corps flags, but you really can't read the numbers.
Even if the star pattern is different, the Confederate battle flags look a lot alike.
Unless it is one, large letter or number, you can never read what is written on the flags. Mottos and place names could just as easily be "Eat at Joe's."
Different flags stand out (the Confederates were especially good at varying their flags), but similar flags tend to look alike. There is no point for making five slightly different flags for five Virginia regiments.
At 15mm, however, you do notice all the differences you don't notice at 6mm. I imagine the issues I'm pointing out about 6mm flags will be even more pronounced at 3mm.
Good Luck!