FYI, I would rent the car for getting to Bled if you are going to rent the car anyway - even though getting to Bled from Ljubljana is easy by bus (or even by train), if you have a car you can take scenic detours see some beautiful scenery and little towns you'd miss if taking the bus. Consider detouring through the town of Skofja Loka on the way to Bled, and drive the scenic detour up through the mountains through Jamnik and Kropa - one of my favorite experiences in Slovenia. (Which is why I mention it so often!)
Get quotes on cars doing both ways: two cars or one car with the one-way drop fee. Sometimes the fee is small enough to make it worth the hassle it can save. Sometimes not.
To get quotes for each country separately, try EconomyCarRentals, Kemwel, and Auto Europe (which now charges the full price of the rental up front when you make the reservation, something I'm not crazy about even though it is still refundable 48 hours prior to picking up the car). They are brokers that reserve cars for you with car companies. I used EconomyCarRentals once and was satisfied (got a car with Oryx, a Croatian company), but they won't book a car for Slovenia dropped in Croatia.
For rent in Slovenia, return in Croatia, look at Sixt - their one-way fee should be obvious on their website if you check prices. Some have rented with IdealRent, a Slovenian company, which supposedly charges no one-way fee, but having seen a quote once, I think they just build it into the daily rate.
If you want to rent two cars, you could drop the car in Koper and take a bus from there to Rovinj - or a transfer with the Slovenian company GoOpti.
Expect to pay smaller one-way drop fees even for the two individual rentals if you rent for short periods. I've never paid a one-way drop fee in Croatia or Slovenia just because my rental periods were more than four days. So you might wind up not paying much more for a single rental with a bigger one-way fee. Just check quotes various ways, see how it works out.
