We had a very good experience with Sixt Rental Car from Ljubljana airport. We got a great car (Opel Astra) with a navigation system and drove it all over the place--it handled well (and it was fun to drive a manual transmission again). We did have to pay an extra fee for a second driver and because we were traveling outside of Slovenia, but it was still pretty reasonable overall. The staff on our arrival was great... we had a friendly woman whose English was very good. On our late night return, one week later, the guy was okay, though he seemed a little put out when we asked him to come look at the car and give us the all clear before we left the premises. He had said it was just okay to leave it in the garage, but I wasn't comfortable with that, so we asked him to leave his desk and come to the garage.
One little drawback is the walk to place to pick up the car, which is beyond the parking garage.
Comments based on reading others' reviews:
I will agree with others, that the insurance deal was a big pain. We turned down all their insurance offers, and they did put a hold on my credit card, but they lifted it when upon return of the car.
I took tons of pictures of the car when we checked it in and asked the guy to log all the damages we found to ensure they were documented.