Hey, these look totally sweet! I don't think it's worth it to make them bigger, as it will indeed both clutter the messagescreen/graphs, and look nasty on maps with small provinces. The latter can be fixed by fiddling with defaultmapzoom for the .map-file, but I'm not sure it's worth it... To me, these smaller ones look great already. Oh, yeah, and if the flags are much bigger, they'll look humongous in comparison to the other symbols nearby; the fort and such.
Hey, make some GUIs to go with the coats of arms, while you're at it!
