It was just a suggestion. I figured that Flanders was an entity before anyone referred to the Dutch, and their flag was distinct enough from France and Germany that it would be a good fit. I'm fine with keeping the orange Dutch flag and COA, though - it makes some of the color issues easier to deal with.
I'm not adamant about any of the flag suggestions I made; I was just trying to get some ideas out there. I think that what we've got so far is pretty good for accuracy; we're just going to have to do something with the colors of stuff on the map - especially since Germany, Austria, and Bulgaria are all likely to share borders and have nearly identical colors. The modern Bulgarian flag is red, white, and a sort of mint green - could we use the COA on a mint green background? For Hungary, as it's got a similar red to Poland, Venice, and Russia/Moskva, how do you feel about red on a gray/silver background, with a dark gray as the map color?
I'm going to propose that we use bright and historically unusable colors for the independents - the aztec green, bright pink, that sort of thing. There's no reason that they should be gray other than to indicate neutrality, whereas we can use a couple of shades of gray for our civs - Germany? Hungary? which we wouldn't dream of using other ends of the palette for. For those worried that the reds and blues are too close together, keep in mind that the flags may look similar, but a larger swath of territory will make the color difference more obvious. As long as we can avoid similar colors for civs that spawn next to each other, we should be ok.