Help with 13 Day Croatia Itinerary - Stops, Must Sees with a little R & R in between

Hi Elenik. Welcome to the forum.
13 days is a comfortable amount of time for your itinerary and the suggestions here might open up a few more possibilities.
Zagreb for two nights is a good amount of time. You can pick up your rental car on the day you depart and start out for Plitvice Lakes. About one hour from Zagreb, consider stopping in the village of RASTOKE which is a village of traditional wooden houses built around the waterfalls and the same river that flows to Plitvice Lakes National Park. RASTOKE is just north of Slunj and is a great place to stop for a picnic or have a snack at one of the local cafes.

I booked one of the Plitvice Lakes National Park hotels- the Hotel Jezero—for its swimming pool & sauna. It offers free parking for guests and breakfast and will give you quick access to the park during the afternoon of your arrival and again during the morning the next day for one admission ticket. You may find one night at Plitvice Lakes is enough when it’s spread over these two time periods after the daytrippers have departed ( the big crowd crunch is between 11 am and 3pm). The park is open in September from 7am until 7pm.
From Plitvice, Zadar is about a 2-hour drive and two nights should be fine here.
After seeing Plitvice Lakes, Krka National Park might become optional as it’s not quite as impressive and swimming is no longer allowed in the waters of the park. Šibenik makes for a great stopover for a couple nights, although you could also stay in a beach town like VODICE that is connected to Šibenik in 20 minutes by road and in about one hour by local car-ferry. Vodice is flat whereas Šibenik is built on a hill with a steep pitch so keep that in mind if reserving a place there. ( we’re staying near the beach in September to avoid all the climbing). Matrinska Beach and Jadrija Beach are nearby and excellent for families with kids.
Split is next and Split is all about Diocletian’s Palace— the palace built for the only Roman Emperor ever to live long enough to retire. It’s a mesmerizing place that looks like an intact Roman forum— including the completely intact Temple of Jupiter. The Roman ruins here are much better preserved than most of the ones in Rome itself.
If the kids get bored with it all, the sheltered, shallow-water BACVICE BEACH with snack bars & showers is a great place to spend an afternoon. It’s just a 15-minute walk from Diocletian’s Palace.
HVAR TOWN is just a one-hour journey on the Krilo Catamaran or TP Line boats. I’ve stayed near Amfora Beach for 3 nights and it was one of the best stays in Croatia. Amfora Beach is about a 20-minute walk from Hvar Town’s ferry port along Hvar’s beautiful promenade. If you stay on Hvar— and you have the time to do it— I would suggest staying just outside of town on a beach you can swim at.
You have a decision to make at this point because you can either continue to KORCULA TOWN on the catamaran in 90 minutes and then be in DUBROVNIK in another 1:45 by catamaran, or you can return to Split. You can either overnight in Korcula Town or continue to Dubrovnik all in one go. The advantage of taking the Krilo catamaran is that — even if you don’t disembark in Korcula Town— you will see the town as the boat encircles the town to dock.

I haven’t yet been to Brac, but did a Split-Hvar-Korcula-Dubrovnik trip that was recommended by my Croatian neighbor.

The website to check ferry/catamaran schedules in Croatia is www.CroatiaFerries.com
You will find great deals this September on beachfront apartments and hotels in Croatia because it looks like the demand is not as great as the supply this year. On Booking.com I keep seeing falling prices for accommodations in Croatia.

Have a fantastic trip!

My short answers to your questions:
- For this trip, 1 night in Plitvice is enough.
- Skip Krka for sure; it's redundant and Plitvice is more exciting. You could consider adding on Mostar if that interests you.
- Drop the car in Split and take the ferry from Split to Dubrovnik, with a stop on one of the islands.  The car is a hassle, unless you want to be able to drive to other towns on Hvar Island, for example wineries or lavender (most people on abbreviated trips don't have time for this).
- 100% spend a few nights in Hvar or Korcula!
- How do you plan to get to Kotor? You could rent a car again in Dubrovnik.

Is that a mistake with your dates?  June 15 - July 8 is more than 3 weeks..  First off, you may want to make your plan based on what accommodations you can get at this point.  Booking.com is good for Croatia, and many (but not all) bookings are refundable until days to weeks before the trip, which is good while you are figuring out your itinerary.  I have not been to Zagreb, Zadar, or Krka.  On my trip, I prioritized Plitvice, Mostar, a brief stop in Split to see Diocletian's Palace before our late afternoon ferry, Hvar, and Dubrovnik because they seemed to be the top highlights.  I could not fit in Kotor but I will return to this amazing area of the world. I was very happy with my choice, but of course your mileage may vary.  If this is your first time to Croatia, I would recommend only 1 night in Plitvice.  There is not much else to do in that area, and as Rick recently said on a Monday Night Travel (regarding something else) "diminishing returns" to stick around a place when there is so much more to see in a country.  You can see Plitvice in the afternoon on arrival day, or first thing the next morning.  A few hours in Split before the ferry was enough of a taste for me on my first trip, I was so glad we stayed on Hvar for a few nights instead.  I was torn between Kocula and Hvar and was happy with Hvar.  We had an amazing day trip boat ride to Bisevo and the blue cave, one of my favorite travel days ever.

Kenko has provided a very comprehensive answer and I would second all of it. I might give some consideration to two nights in Plitvice just because it might be easier to manage with the kids. You’ll definitely want to be in the park very early or late to avoid the crowds. I might get a bit nervous with little ones on the walkways if there are lots of people. Hotel Jezero would be a top choice with its amenities and proximity to the park entrance. Considering you might still be a little jet lagged, some extra time here with the kids wearing themselves out at the pool could be helpful.

I don’t have any concrete recommendations, but the area around Plitvice is a popular outdoor destination. I recall seeing a number of signs for a local action park/zipline, could be worth checking.

I will throw in what little I know. I have been three times but it takes more than that to understand a place well enough to be much help.

Plitvice in June. Unless I were willing to get up early and head to Plitvice and deal with the crowds at 10 or 11 am ... I just wouldn’t do it. In June, it’s going to be crowded all day, just to what degree of crowd will change. It is taking 2 days out of your journey for 4 hours of looking at water. And yes, I have been .......... and in July ......... but we were randomly blessed with a manageable size crowd.

Split. Well, I've been to Croatia 3 times but Split only twice. The first trip was short and okay. The second trip was July and it was a freeking zoo full of drunk trust fund brats. Fine, as long as you go home before dark. Others that have gone say i am exaggerating. Isn’t true. Yup: https://captainsboatpartysplit.com/blog/is-split-a-party-town/ But that aside, it’s a lovely place and worth 2 nights. 3 …….mmmmmm not for me.

3 nights Dubrovnik (day trip to Kotor). That means you have two days and a few extra hours in Dubrovnik. Kotor is a 6+ hour round trip to see something that looks like Dubrovnik but is smaller and less impressive. You might enjoy 3 or 4 hours there. Another idea is hiring a private transfer to Perast. Do the island boat, blue cave, maybe the sub base boat trip. I think the kids would enjoy it. And it will save a little travel time. Although Perast might be a bit busy in June. But a good guide/transfer knows the work arounds.

If you were to skip Plitvice I would go hunting for a place away from the tourist for a few days of rest. I would suggest but someone would yell FOUL!!! Croatia is beautiful, but the world has found it and you will be dealing with crowds quite a bit.

The view and the beauty are so good, I would rather be looking out the window than watching the road. Hire transfers. Its worth it. I am going to suspect the Croatia experts here can help with that, if not, I know one. I also know a good guide in Dubrovnik if that interests you.

The OP did their research and has included the UNESCO World Heritage Sites of Plitvce Lakes National Park, Šibenik ( which, by itself, has 3 World Heritage Sites), Diocletian’s Palace in Split, and Dubrovnik’s walled Old Town.
Plitvice Lakes is also widely considered Europe’s most beautiful national park.

Thank you so much for all your tips.
I've added a little more detail to the itinerary and hoping you can further guide me.
I'm wondering if I'm packing in too much. Please see my questions --> with every section/town

Zagreb - 2 nights

*Plitvice Lakes - 1 night *
- Afternoon & early morning
- trip to Rastoke Settlement

*Zadar - 2 nights *
- day 1: old town
--> which of these are most recommended? glass museum National Musuem, Dukes Palace ?
- day 2: Kornati National Park (Can we do this on our own or should we take a guided tour?)
- day 3: Beach 1/2 day
--> Which, if any and why? Vodice, Pag Island, Punta Skala, or Dugi Otak or other?

• Sibenik- 2 nights
• day 1 Old Town
• day 2: Sibenik Archepeligo ( Zlarin, Tijat, and Prvić) --> is this recommended? Is it better to use a skipper or do on our own with ferry/water taxi?
  
• day 3 Skradin, Primostin, Trogir to Split --> Should we skip the Krka National Park or go and take the 4 hour boat trip (Rosi Slap waterfall) or spend more time in Sibenik/Split?

Split - 2 nights
- --> Do you recommend we do any of these: Trip to Island of Trogir or Visit coastal town of Omis
--> Getting to split: Which is better and why : Car/Bus via Mostar OR ferry/catamaran to HVAR and/or Korcula
--> Which is better to stay over HVAR/Korcula - this means we lose a night in split *.

Dubrovnik - 2 nights

--> Then it was suggested that we don't hire a car during our trip, but rather to enjoy the scenery. Which parts of the journey are cheapest to use private transfer (please provide recommendations) or should we just consider the bus?

I think you choose wisely. Bus or transfer? Up to you, really. Get some prices on the transfers and compare cost and time and see if the transfer affords you any stops along the way thst would be interesting. There is Daytrip.com, good but a bit pricey, and I pass out one company name for this sort of thing way too often but so far I haven't seen an alternative offered. Competition is always good. PM if you want the name.

I agree with other comments that Krka is not as impressive as Plitvice. However, your kids might enjoy the boat ride into the park. There is a 'beach' with swans at the river to relax at after you visit the park. We stayed in Skradin, but there is more lodging in Sibenik. I highly recommend driving to the Sokolarski Raptor Center for the tour. You could do this on your Sibenik 'Old Town' day. We stopped at Primosten and found it more charming than Trogir. Your kids would enjoy the beach there. We also stopped at Klis Fortress outside of Split. Froggyland in Split is interesting! Two nights in Split really only gives you one full day there. We spent 3 nights in Mostar and loved it but I'm not sure it's worth stopping at, with border crossings, between Split and Dubrovnik for just a few hours. You could stop at Omis or a beach near Markarska when driving to Dubrovnik. That would be easier than rushing to spend one night on an island. You definitely don't need the car in Dubrovnik. Make sure all your lodging except Dubrovnik has dedicated parking for your vehicle.