Wonderful Area
I know this is an old thread now but having "done" Slovenia, Croatia and Bosnia this summer I would like to add my bit.
Basically, go for it. For the last few years my wife and I have travelled to the more Eastern areas of Europe and have had great holidays. This year we travelled through Germany (first night near Karlsruhe), then Austria (stopping at Salzburg for new rear tyre - cheaper than UK) then the first MUST DO section, into Slovenia over Vrisic Pass. The BMW dealer in Salzburg said it was the only was to go. We were going that way anyway and he was right. Having "done" Stelvio and Transfagarasan this road is right up there with the best and has the most amazing views. Shame my wife dropped her 650 GS on one of the 50 cobbled hairpins though.
Obvious visits in Slovenia are Predjama castle, Postojnka caves and Ljubijana, then on to Croatia and Rijika. We then followed the coast of Croatia all the way to Dubrovnik. The coast provides an amazing ride with the wonderful Adriatic on one side and mountains on the other. We stopped for a few days on a big campsite at Omis and then a couple of nights in a hotel outside Dubrovnik. Note that to get to Dubrovnik it is necessary to drive through a little bit of Bosnia and there is nowhere to get local insurance for Bosnia at that entry point - so we carried on without it.
Omis was a great stopping point. Big campsite on the sandy beach with bar and decent restaurant. Very touristy town nearby and a good base for some great rides into the local mountains. Once you get a couple of miles from the coast you lose the tourists and see the real Croatia. Dubrovnik was solid cruise ship tourists but the old town was still a must visit and the drive there made it worthwhile.
After Dubrovnik we turned back north and then inland to Bosnia and Mostar. The main border crossing does have a means to buy insurance (10 Euros per bike) and all our docs were checked at the crossing so we were glad we bothered. The south of Bosnia is a bit depressing but Mostar made it worthwhile. Finding a room in Mostar was tough we we eventually got one a few minutes from the famous bridge for 50 Euros and an evening sitting at a restaurant terrace overlooking the famous bridge was a highlight of the trip.
After Mostar the Bosnia roads get more interesting, going through gorges and over mountains north to get to Plitvice National park back in Slovenia. We travelled via Jajce in Bosnia which guides show as having some great waterfalls but they look better in pictures than in real life.
After visiting the park, also a highlight, we turned north via Maribor, Salzburg and then home.
The whole trip was 18 days. Total mileage about 3500. Some night were spent camping and others in hotels. In general we found camping to be expensive compared with UK but sites were very good. Hotels were very reasonable costing only 40 - 50 Euros for a night. Roads were good everywhere and mostly pretty deserted. All our navigation was done by Garmin satnav. In Bosnia it only shows main roads but it still had enough info. plan and ride where we wanted to go. We needed to buy road tax (Vignette) for Switzerland and Slovenia. A couple of motorways in Croatia were toll roads and some Swiss roads still charge an expensive toll in addition to having to buy a vignette. Both my GSA and my wife's new 650GS performed perfectly.
A couple of bits of video on YouTube are:
http://www.youtube.com/watch?v=cht9WFblVpc
This shows a bit of Vrisic Pass. Unfortunately my GoPro battery died before the best bit and my wife won't let me publish the bit showing her dropping her bike.
http://www.youtube.com/watch?v=CP-UXVzN748
This shows a section of the Croatian coast south of Omis. Its a wonderful ride.