starting where?

We took a train to Ljubljana and spent 2 night there with no car, then rented a car and made a loop by Lake Bled, spending 2 nights in Kobarid and then back to Ljubljana where we turned the car in. We rented from Budget at the hotel in Ljublijana, not at the airport. We then walked over and caught a train to Rijeka (3pm daily, I believe) where we walked over to the Quay to rent a car from Oryx for 10 days. We used that to drive all around Istria, to Plitvice, Split, Dubrovnik, Mostar and to Kotor. We returned the car in Dubrovnik and flew out of the airport there. We found Oryx a great company to deal with. We let them know in advance that we would travel to Mostar and Kotor and all of our paperwork was in order for every border crossing. We even paid a little extra to have an awesome wifi hotspot. If you can make Dubrovnik your last stop, you won't need the car once you are there. We paid to park it there, and in Split and in Kotor, but were still glad to have it otherwise - we weren't trying to be 100% cost efficient, but we were avoiding cruise crowds to make the most of our time... We were there late May and we did a couple of kayaking trips, but no swimming. I did wade in up to my waist once. Non-southerners would no doubt have been quite comfortable.

When I visited Slovenia and Croatia in 2014, I flew into Zagreb, rented a car at the airport, and drove immediately to Ljubljana. I kept the car for two weeks, dropping it off in Split, and then visited Hvar, Korcula, and Dubrovnik, traveling by ferry. I flew home from Dubrovnik. With just two weeks total, you could do something similar. The drive from Zagreb to Ljubljana is just about 2 hours, and I was not too jetlagged to do that. If you are concerned about doing that drive after your long flight, you might consider spending a day or two in Zagreb first.

I'd tend to start in Dubrovnik--if I could manage the transportation to get there at the beginning of the trip--because it's the place I think is most likely to be overly touristy as you get into June. But it might not make any difference, and it will be a great trip either way.

Just be sure you spend the night before your Plitvice Lakes visit very near the part so you can get an early start there. The car will help in visiting Plitvice either before or after Istria, and it certainly will be handy in Istria itself.

Great information, thanks!

I would check the price of flights into Zagreb vs. Dubrovnik.

For us in Denver, we had a better price flying into Zagreb, renting from Sixt, and driving for two weeks into Slovenia, Croatia, Bosnia, and Montenegro before dropping the car in Dubrovnik the day we drove into the city.

Zagreb to Dubrovnik is an excellent choice. Zagreb is only 80 miles from Ljubljana and you will avoid the international drop-off fee. Just make sure to buy the vignette (toll sticker) for Slovenia before crossing the border, as your Croatian rental will not be equipped with one. I'd keep the rental for the entire Slovenian leg, you don't really need it for Ljubljana and Lake Bled, but it will be useful for all the other places you'd visit. I recommend the Julian Alps drive into the Soca Valley and then continuing down to Istria from there, some great scenery and wonderful regions along the way. Make sure to stop at one of the many agriturismos in the area to enjoy some excellent home-made meals.

As far as Dubrovnik goes, I recommend checking the cruise ship schedule and plan to visit on a low-activity day. It makes all the difference. I'm inclined to recommend starting in Dubrovnik and working your way northwards, but by late May the weather is lovely everywhere so it doesn't matter as much.