We will be arriving in Slovenia, Lake Bled, in early October, 2018. Want to rent a car for several days, returning it in Ljubliana. Then rent a car for2 days in Croatia; Zagreb to Split. Suggestions re: rental company to use, best pick up/ drop off options. Finally, RS talks about large drop off fees in car is rented in Slovenia and dropped in Croatia. Has anyone know of a way to get around this?
Yes, the way to get around it is exactly what you said you were planning to do: rent two different cars, one for each country. You generally only get dinged for a dropoff fee if you pick up in one country and return in a different one.
I rented a car in Ljubljana and dropped it off in Portoroz (on the coast, just barely inside Slovenia, near the Croatian border). Took a bus from there to Rovinj in Croatia. Rented a second car there, dropped it off in Split. It worked out great. The logistics of the bus from Portoroz to Rovinj were non-trivial (consumed a few more hours than I would have liked) but it saved what would have been the very significant drop-off fee which was something like 700 Euros, so I happily accepted that trade-off. YMMV.
If you are going to Zagreb anyway, then it should not be a big inconvenience to drop the first car at the Ljubljana train station (Sixt has an office literally in the station) and pick up another one in Zagreb (maybe not at the train station). You can take a bus to Zagreb too (I'd prefer the train myself). The Zagreb bus and train stations are not quite adjacent but connected by a tram. I'm not sure which rental agencies might have close to either the bus or train stations there.
Another train option is taking a train from Ljubljana to Rijeka and pick up the car there - I did that on another trip to Croatia, because I wasn't headed to Zagreb this time. This option makes more sense if you are going to say Istria first (about an hour from Rijeka to Rovinj by car) and just prefer trains to buses; there is a direct train 2X a day to Rijeka.
Another way to "get around" this problem is to fly into Zagreb to start and rent the car immediately and head to Slovenia, then return the car later in Croatia again. I take it that by now you're already locked into flights for October.
I usually use https://www.whizzgo.co.uk/ to plan my car rental schedule. The search function is pretty good, but if you require more advanced options and assistance, I suggest you call the support. In my experience, the prices seem fair. However, I am not sure about your setup. Better check it out.