Which car companies have you tried? Some charge a per-day fee capped at some maximum. I was once going to rent a car from Fleet (wound up changing my plans) and they charged 5 euros per day, 50 euros maximum per rental. I wound up renting with Oryx instead, and they charged a flat fee of 40 euros including VAT for the cross-border fee. (These prices are two years old, perhaps they have gone up.) The fee is less painful for a longer rental, of course.
I wouldn't worry about the fee. Just consider it part of the total price of the rental when comparing prices between companies - and choose the best overall price. What other choice is there? The trick is finding out what the cross border fee really is, and that may require snooping carefully on their website or emailing them directly (as I did) to find out what the fee was, so I wasn't surprised by it later.
As for one-way rentals in Croatia: expect a drop fee if you have a short-term rental but not for a rental longer than a few days. I've done two one way rentals within Croatia and never paid a drop fee, but both were more than a few days. A hefty one-way drop fee when dropping the car in different country from the one you rented it in is routine.