Need input/advice/suggestions for potential Croatia itinerary

-Fly into Zagreb, rent car (anything we should see in Zabreb?) We spent a couple of days in Zagreb. Many of the palaces, churches, and museums are closed because of the 2020 earthquake, but we enjoyed the Museum of Broken Relationships, Tkalciceva Street, the Botanical Gardens, and the architecture. We also stayed in the best apartment rental we have EVER had (and we've rented many).
-Drive to Plitvice National Park (1 day? stay overnight?) Stay overnight at one of the hotels in the park. We stayed at Hotel Jezero. This will give you two entrances to the park (each) included with your stay, so you can go late afternoon after you arrive and again in the morning. You can avoid most of the crowds this way. We did this in May, and there were times no other people were in sight.
-Drive to Istrian Peninsula, Pula: Roman amphitheater and ruins, stay overnight)
-Drive along the coast stopping at coastal towns of Zadar (Public Art: Sea Organ and Sun Salutation), Sibenik (Michelin Star Restaurant: Peligrini, St James Cathedral) (2 days) We stayed in Zadar and enjoyed it very much. Besides the Sea Organ and Sun Salutation, there are Roman ruins. Also, the sunsets are beautiful. Alfred Hitchcock claimed they were the most beautiful sunsets in the world.
Edited to add that the Sun Salutation can be viewed only after dark. During the day, you can see the solar panels embedded in the pavement, but that isn't interesting. After dark is when they light up and "dance" and people are enjoying them. There's almost a festival atmosphere.

(Are there any other towns or sights along the way to savor?)
-Drive to Split: Diocletian's Palace. (2 days)
-Use Split as base camp to visit Medugorje. (1 day)
-Possibly visit Mostar in Bosnia Herzegovina after Medugorje (1 day)
-From Split, visit an island or islands? Korcula, Brac or Hvar? Advice please on which one or options? How many nights? You will get different opinions on islands. Brac is a bit more challenging to get to that time of year. A lot of people love Korcula. We stayed on Hvar, in part because of the ease of travelling between there and Split. We were also able to take a tour from there to the Blue Cave (recommend!). You can do this from Split, too, but it's farther.
-Drive to Dubrovnik: (2 days) Add a day or two to Dubrovnik, if you can. We adored Dubrovnik. We also enjoyed spending an afternoon on Lokrum Island.

I suggest that you book open-jaw or multi-city airline reservations. Fly into Zagreb and fly out of Dubrovnik. This will save you time backtracking to Zagreb.

Just a few things.
If you are arriving from the U.S. to Zagreb, you might consider spending your first night there before getting a car and driving. The road from Zagreb to Plitvice was nice, but you would still be coming off jet lag. Getting used to a new country, different driving styles, and a different car usually requires extra concentration.

Yes, stay overnight. If in Zagreb, you may arrive late afternoon and could enjoy the park the following morning starting early. My friend and I stayed in a 2 bedroom apartment not far from the entrance - others suggest staying in a hotel on the grounds. My decision was based on cost and space.

Others are not enamored with Pula but I really liked it. I enjoyed Zadar as well and used one day as a day trip. You could enjoy the old city area of Zadar itself in one full day.

I can’t speak to making the day trips to BiH from Split. I did visit the Blue Cave via speedboat from Split - again time of year might matter.

I would say use ferry schedules to determine an island visit. People say your timing might be a bit early - but I don’t know, as I was there late September. I love Korćula, but Hvar is lovely and might be quiet enough at that time of year.

If you do choose an island stay, you could return the car in Split and ferry from Split to the island and then ferry on to Dubrovnik. It would save a few days of rental.

I used UniRent for Dubrovnik to Split for about 2 weeks. But they have an office in Zagreb also. The return IN Split might be harrowing (but very interesting) if you haven’t driven enough to pass the “harrowing” stage. 🤣 So maybe returning to the airport would be better. The city location for Dubrovnik was easy.

Get the parking app. It is wonderful. https://paydo.hr/ I also haven’t checked timing on any of your routes, so no comments on those.

As someone mentioned, if don’t already have tickets, you could check flying multi-city.

I'm not a great adviser because I hate road trips, but I love Croatia so here goes.

Day 1, Zagreb is an underrated city, and even if some museums are still closed it's worth a day, plus you should shake off any jet lag before driving long distances.
Day 2, I would overnight to avoid too much driving that day. Check maps to see if it makes more sense to see Plitvice before or after Istria.
Day 3 I would consider saving Istria to give more time elsewhere in the plan. It's a lot of driving!
Day 4-5, Zadar and Sibenik are small and I think this part works
Day 6 You might need to do some laundry at this point, relax and enjoy Split
Day 7-8-9 Rather than go back and forth into Bosnia, I would stop here en route to Dubrovnik, perhaps overnight at Mostar. There are some sights in Hercegovina that you might want to include, waterfalls and some religious sites.
So, put any island day trips out of Split before heading south. Korcula would make more sense if you were traveling by sea because it is between Split and Dubrovnik, but Hvar or Brac would work. If you have room to add an overnight, why not? It will be quiet but not shuttered.

Why go to plitvice then backtrack to istria?

I think your much better off going to istria and then heading to plitvice on the way down the coast rather than backtracking (and yes I know plitvice isn’t on the coast but that’s a huge backtrack Zagreb - Plitvice - Pula

Zagreb is a logical place to fly into to start a Croatian trip, but it is possible to fly into say Venice and take transport to Istria and rent the car starting there. At least, I would consider flights into Venice and see how they compare for you vs. flying to Zagreb. Sometimes it doesn't make much difference, sometimes it does. You can take a ferry from Venice to certain cities in Istria for example or a bus (also a Slovenian shuttle service called GoOpti might work). Of course, you could spend your first night in Venice and shake off the jet lag there...

Some people do love Zagreb. I'm not one of them. I've been there twice (second time recently) - and although I definitely think Zagreb is worth visiting if you are passing through, it's not a place I'd rank highly in Croatia - just my personal preference. It's kind of a bland big capital city. On the other hand, it's probably the most "real" place on your Croatian itinerary since most of the spots are vacation stops with a lot of tourists. Zagreb is the country's capital...but I wouldn't have felt I was missing much by skipping it.

Korula, Brac, and Hvar are all nice islands. Hvar and Brac are super easy to get to by ferry. Brac and Hvar are probably detours you'd take from Split, then back to Split and drive south to Dubrovnik. Korcula is on the way south. You could ferry from Split with the car to the town of Vela Luka on Korcula, then ferry from Korcula Town across to Orebic (short ride) and then south to Dubrovni...or ditch the car in Split and take a catamaran from Split to Korcula Town, then a catamaran or bus from there to Dubrovnik. (And yes, try to do an open jaw flight into one out of another city vs. the round-trip or vs. two one-way tickets.)

We really enjoyed Zagreb! It reminded me of a smaller and much less crowded Prague. What is nice about Zagreb is that it is very different architecturally from Split and Dubrovnik. So including Zagreb in your itinerary gives you some diversity. We visited the Museum of Naive Art, which is very interesting. This is Croatian "peasant" art. We enjoyed the colorful and fun market in the main square. We enjoyed exploring Upper Town and Lower Town, taking photos, stopping for drinks and lunch at one of the many outdoor cafes on Tkalciceva Street.

We had two favorite restaurants in Dubrovnik: Kopun and Taj Mahal, a Bosnian Restaurant.
http://www.restaurantkopun.com/
https://tajmahal-dubrovnik.com/
Their websites indicate they are "temporarily closed." Hopefully this means they are closed only for the winter months.

I would take the Rick Steves Best of the Adriatic tour for 14 days. It was an outstanding tour!