First things first. I really like what you're doing with this map.
1. You still have the issue of smaller countries/city areas being hidden. I'm not sure if a line from the territory name to the city would look tacky, but something probably needs to be done. I'm talking Lux., Liech., SM, VC, Andorra, and Monaco.
2. I would probably recommend moving the Corsica, and Balearic Islands army circles so that the colour of the island underneath is evident.
3. a couple of your water routes need clarification. The first ties in with point one above. Monaco to Corsica. Maybe I'm being silly, but probably a few people will think it connects to France. If you can clear up the city thing a bit somewhat, then maybe this issue goes away.
the second one is the England to France connection. I just didn't see it the first time around. Maybe move it so that the connection is located on the west end and it might become more evident with that open water around there.
I just noticed that you might be able to say the same thing about the other connections in the British Isles. They're probably OK but if they were more visible somehow (maybe just location-wise they just aren't in the optimal spots) that couldn't hurt. Probably the same thing could be said for the Malta connection. With so few dots, I just didn't notice it. Obviously it's going to connect there, but from a visual standpoint, I think it could be better.