We will be traveling from various countries in Eastern Europe by public transportation. However the last part of our trip is Croatia and Slovenia. Our original thought is that we would travel Croatia (Zagreb, Plitvice Lake, Istria) and then travel to Ljubljana/Lake Bled in Slovenia and back to Pula to fly out. (only because cost to fly out of Pula is nearly half that of flying out of Ljubljana). Was looking at public transportation and feel like there is a lot of time wasted/back and forth. Was thinking it might be best to rent car in Zagreb and travel around Croatia, take care to Ljubljana and return car in Pula (thus avoiding the crazy drop off fee in another country). For those that have traveled this area, does that make sense? We already have a packed schedule (yes, we know but have to take advantage of being in Europe!). So trying to utilize time but also have to look at financially what makes the most sense! Any suggestions would be greatly appreciated!
I haven't driven in that area so can't so for sure how well your plan will work.
I wonder, though, whether it's really cheaper to fly out of Pula rather than Zagreb? ViaMichelin indicates that you can drive from Ljubljana to Zagreb faster than to Pula, and--should some sort of disaster occur--there's both rail and bus service between the two capital cities.
Give rough plan with number of days or dates you have to visit please.
There are many factors to take into account, but most of this leg appears to be more rural/small town, which would lean toward a car, if only due to issues with public transport and the lack of direct connections. Taking public transport may mean rethinking the order of your schedule, maybe even changing where you go.
If you go the rental route, you may want to delay getting the car until you leave Zagreb, then ditch it before Ljubljana, or stay outside larger cities and take public transport in to daytrip. Also look into costs and the ability to take a rental across borders; as well as it looks like you would be renting in one country and dropping off in another, that can be expensive. Find a good rental agency and discuss your plans with them.
You may also want to consider that the question is not "Either-Or", it could be both. Consider using public transport for longer direct connections (Zagreb to some point in Istria for example) then rent a car for a day or more to explore the area, then public transport for the next long leg.
Publick transport is fine. You just have to coordinate more. From Split Zadar or zagreb u have many busses to Plitvice lakes. you just have to check your accommodation and do they offer a shuttle to the entrance. it is a huge park. for example, you come to the hostel at afternoon and in morning by shuttle you go entrance to lakes and afternoon you catch a bus to next destination. look for hostels with a kitchen too or bnbs.
Car rental is very cheap in offseason. You may consider that option too.