I like it, Yugoslavia could use some love. I must say I liked the more colorful version you posted in HCS more
I understand the bonus area divisions, but Croatia, Bosnia-Herzegovina, and Serbia (especially Croatia) are by no means feasible to obtain and hold until endgame. I suppose you could just chalk it up to the preset political/ethnical boundaries or the geography, but nonetheless I'm not sure how well this map will play, with the peripheral small bonus areas and the large, unobtainable ones in between. As for the gameplay elements you've included, I like the Adriatic Sea concept, but am not fond of the capitals. The auto-deploys only make the smaller bonus areas only easier to hold (since their capitals are all within a bordering territory) and worth more. Belgrade... It's a neat idea with it assaulting all the capitals, but I have a hard time seeing first, the reasoning behind it (aside from just a nice gameplay addition), and second, seeing it be too effective. As already stated, all the capitals in the smaller bonus areas are within a border territory, so they will be well protected, therefore, it can't really be used as a tool to break bonuses, merely a way to skip over a few territories to Zagreb or Sarajevo, the only two possible capitals to attack mid-game.
Something gameplay-wise needs to be changed, as the bonus area boundaries really aren't working with standard gameplay. One solution, I think, would be to use the "+X per Y territories in one bonus area" approach. In this way, you could even keep the capitals and such (the auto-deploys now being worth just a tad more, yet not being too unfair, given the smaller bonus areas would be worth less, and wouldn't necessarily need hefty protection) and it would increase the value of the formerly near-worthless middle bonus areas, Croatia, Bosnia-Herzegovina, and Serbia. Starting positions and the bonus per territory in each bonus area could easily (more or less) be set to balance things out: +1 per 2 for Slovenia, Vojvodina, Montenegro, Kosovo, and Macedonia, +1 per 3 for Croatia, Bosnia-Herzegovina, and Serbia. You could even do +1 per 2 in all bonus regions, but it would take a little more work with the starting positions.
Small nitpick: If you prefer to keep the gameplay as is, I'd suggest for Macedonia, either removing the mountains between Polog and West Kosovo and up it to +3, or merge two territories and keep the +2. If you decide to go the +X for Y route explained above, I think the mountains could still stand to be removed.
P.S. I just realized what I suggested is strikingly similar to your and Helix's Korea map, lol.