I've read that the surcharge for picking up in Slovenia and dropping off in Croatia can be hundreds of dollars. I checked kayak.com and sure enough, it's about a $500 extra fee. But the only option it listed in Sixt. Does anyone know of another rental agency which has a more reasonable surcharge? At that price, I'll just return the car to Ljubljana, take a train to Zagreb and rent a new car. But it would be really nice to avoid those extra logistics.
I doubt that you'll be able to avoid a high surcharge, but check the consolidators AutoEurope and Gemut.
People traveling from country to country often have to switch over to trains, planes and buses taking them to the next country to avoid those dropoff fees. The rental company has to transport the cars back to their home country to continue renting them.
You haven't mentioned where in Croatia you'd be dropping off the car, perhaps Dubrovnik? I believe some companies charge less for dropping off closer to the border, for example in Zagreb.
Rather than checking brokers, have you tried checking out company websites directly? Look at local companies, too, such as Atet.