Quite a good looking map here! Graphically, I think you need to add a bit of a glow behind your text. In most cases the names of the territories seem to be blending into the territory itself, and in a couple cases, like Antwerpen, the name crosses a border and part of the name is lost in the border. A glow or white shadow effect will have the text pop out.
I think you also need to make the color of the water a more distinctive color(a darker blue, or blue-green) The rivers towards the bottom of the map could be misconstrued as a regular border. Also the ocean color is almost identical to the color of Vier Ambachten bonus.
I know you increased the size of the mini-map, but it gets in the way of the Oostburg-Broeklburg connection. Try and keep it as big as possible, but you may have to shrink it down a smidge to get out of the path of the line.(mostly)
Gameplay wise, your bonus values seem a little low in some places, but not terribly so, and since this is a smaller map, you don't want to get too high, especially with the capital bonuses. It just seems to me that there are a lot of connections between bonus regions, especially in the small central regions of the map. For example: Rijks Vlaaneren is a +1 bonus where all 3 territories are borders into 5 territories in 4 different bonuses. It wouldn't be worth holding it to get just 1 extra army, even with the extra +1 for Aalst.
Why is Kortrijk completely cut off from the rest of its bonus? A bridge connecting it to one of the other territories in the bonus should be added.
Explain capitals to me some. From what I see, there are 3 capitals in one bonus region, and no capitals in 3 other bonuses. Are these more like areas of major uprising, or rebel strongholds? Maybe just a change in terminology will prevent any confusion, and if you do an auto-deploy as was already suggested it will add nicely to the theme, since you basically have inflamed peasants swelling the ranks of the Flemish armies in those regions.
Hope this helps, keep working at it, the map is quite good!