Yeah, the fee for renting the car in Slovenia and dropping it off in Croatia can be prohibitive.
We did a trip that was almost exactly the same as yours about 5 years ago (although I would recommend against landing in Ljubljana and just jumping in a car and driving off to lake Bled: first of all, unless you are just flying in a short distance, or you're very good at sleeping on planes, I think you will be wiped out upon arrival and in no shape to drive; second, Ljubljana is a charming little city and is worth a day).
About the car: we decided to "beat the drop-off fee" by renting 2 cars, one from Ljubljana to the Croatian border, and a second from Rovinj onward through Croatia. Important! All of the following was true back in spring 2012, but if you want to do the same, you will need to verify that everything still works...
I found what I believe was the closest Slovenian town to the border with a car rental agency for our dropoff point: Portoroz (on the Slovenian coast, near Piran). Dropped our Slovenia car there, then we caught a small bus to Roving. The execution consumed a few hours but it worked out OK. After a few days in Rovinj, we picked up our Croatia car and headed on to Plitvice and beyond. We then went to Rab (which we loved), down to Sibenik, Zadar, Trogir and Split. Dropped the car there in Split, ferry to Hvar, Korcuka, then Dubrovnik. Day trip to Kotor, flew home from Dubrovnik.
It worked out great for us, although the day we dropped car #1 and bussed across into Croatia by bus was a bit complicated and tiring (we had several hours to kill in Portoroz and spent some time wandering on foot with our bags). That bus did not run every day, so check that. Also, the bus stop for pickup in Portoroz was not well marked - it was nothing more than a "park bench" by the side of the road with a tiny "street sign" as the only marker - we had to ask many times to find it and verify it was the right place to be. Finally, about 5 minutes before the bus arrived, about 5 locals showed up and quickly formed a queue, ignoring us. Even though we had been waiting there for an hour, we were at the end of that queue...which didn't concern me until the bus arrived and I saw there were only about 5 empty seats left on the bus. We got the last 2 seats. Had there been anyone else ahead of us in the queue, we would have been out of luck - the next bus for Rovinj wasn't for 2 more days. So, be sure you check for such tricky details and verify everything.
Hope that helps - good luck!