Will be picking up rental car from LJU to tour around Slovenia for 10 days. Afterwards, will take GoOpti / FlixBus to Italy. Should I return the car at LJU or downtown Ljubljana? Which location will be more convenient for the onward journey with GoOpti / FlixBus?

You can choose where GoOpti picks you up at or drop off. If the airport is more convenient for you and your plans, I'd choose that. So much of Ljublana is pedestrian only, of course less so outside stari grad.

If you take Goopti the airport is probably more convenient.

rialtogrl Why would airport be more convenient for GoOpti? Is it because of the pedestrian zone? Would the train station be an OK alternative? It just seems like back-tracking going back to the airport. What am I missing?

Are you ending your tour in Ljubljana? You asked what is more convenient. Driving into Ljubljana to drop a car off at a station isn’t as convenient as the airport, unless you are going to stay in Ljubljana anyway. Goopti will pick you up at the train station, but they are known for being an airport transfer service (this is how they started, as a way to get people to airports.)

Once you have decided where you will end up and drop your car off, then you can decide to best way to get to Italy.

I guess I don't understand your trepidation....You mentioned LJU, so one would think that is part of your consideration...

Perhaps you can let us know your Itinerary plans for Slovenia for what might be a better ending point to return the car.

How are you getting to Italy? That's your first decision. If you use GoOpti, like I mentioned upthread, you can choose the pick up point. As RG mentioned, the service is primarily an airport transfer service though they do other transfers as well.

If you decide FlixBus, perhaps it may be more convenient for Ljublijana proper, depending on location of bus vs. train.

Where is your next point in Italy?

Thanks for the feedback. Sorry I didn't clarify my plan.
Will pickup car from LJU, then head to Bled and use that as a base to tour around for a few days. Then driving to Ljublijana city and use that as a base for a few days to tour the caves. After that, head to Padua, Italy.

Few car rental agencies I checked have offices in both airport and Ljublijana city (by train station). One-way drop-off fee is either none or 10 euro.
Also noted the FlixBus station is by the train station. And GoOpti pickup is anywhere.

So I think it makes more sense to return car in city center?

If you are heading to Padua from Ljubljana without a car, bus will be faster than train to Trieste and then you can take a train onwards. Check ap-ljubljana.si for buses from Ljubljana. Of course, that would mean travelling from Ljubljana airport or wherever you drop the car. If that's Ljubljana station, note that it's a busy area but not chaotic.