Significant other and I visited Slovenia/Croatia/Bosnia in May 2014. A great trip! Rented one car in Slovenia, one in Croatia, and took buses and trains for the rest.
If you have ever used AirBnB, I would consider using it for some of the places on your trip. We had good experiences with it, and everyplace you stay will be quite inexpensive. (Although don't be misled into thinking it will permit you to make meaningful contact with the locals through your landlord. It likely wont). I would not try and use it in Split or Dubrovnik, though.
We started in Lake Bled. Beautiful place, worth an entire long day itself. Saw the castle, walked around the lake, took the quaint boat to the church on the island, ate dinner in town, walked around more, headed back to our AirBnB place.
Drove through the Julian Alps, stayed in a place way up in the mountains above Kobarid, or Caporetto. There is a lot to see for WWI history buffs.
Then drove to Piran on the coast. Also worth the full day we spent there. Saw one of the caves on the way back to Ljubljana.
3 days in Ljubljana. A very pleasant and civilized city. One of the few places in Europe I think I might be able to live permanently.
Took a train into Croatia, and picked up the car. Visited Rovinj and the Istrian penninsula.
Plitvice Lakes takes a full day, and is very worth seeing. I've never seen anything quite like it. Start your day as early as possible to avoid the crowds!
Got to see some very untouristed towns in Croatia, still full of buildings riddled with bullet holes and damage from the 90s war, while driving on the way in and out of there.
Drove to Split, and dropped the car. Stayed two days at a place in Diocletian's palace. Very interesting old town.
Took the ferry to Hvar. Stayed two nights, at an AirBnB place that advertised the best view in Hvar. Lots of steps to climb, but it did have the advertised view.
Took the ferry to Korcula, spent two nights there. Also a wonderful old city.
Took a van to Dubrovnik. It clipped a motorhome going the other way, which was interesting. and caused a couple hour delay. Totally the motorhome driver's fault.
We spent 3 full days in Dubrovnik, and I thought that was about the right amount of time. In the BnB most strongly recommended by Rick Steves. Lots to do and see there. The old town is very interesting, has a lot of history. Have a drink at one of the bars by the Adriatic. The fort at the top of the cable car ride is also quite interesting. It's also worth taking a quick trip through the newer part of the city, the Yugoslav era waterfront, if you have the chance.
Then a bus to Mostar. We stayed at a AirBnB place right on the water that advertised a million dollar view of the Old Bridge. And boy, it's owner wasn't kidding! Best AirBnB experience we ever had. If I were you, I would stay at least one night there, and try to focus on the Turkish cultural things available there.
Then Sarajevo for 3 days. The most interesting City on our trip, with its mixture of peoples and religions, living uneasily together, all still heavily impacted by the 90s war. Flew home from there.
The thing I most wish we had time to do that we didn't do was visit Montenegro. We planned to do that from Dubrovnik, but there were no tour vans available to take us the day we were planning to go. So make sure you have that covered before you get there.
I would consider going without a car from Dubrovnik, to Korcula, to Hvar, to Split. Take the ferries instead. Rent one car for the rest of Croatia as you leave Split, drop it in the last place you are visiting in Croatia, and take a train to Slovenia.
It also almost seems to me that you might not need a car in Slovenia. There are convenient buses/ trains to get you from Ljubljana to Lake Bled and back. And you could easily pick up a tour group from Ljubljana to the cave/castle.
