7 nights in Croatia: Zagreb to Dubrovnik

June is not uber-high season in Germany but it does border on iznad-high season in Croatia. So go with it and have a blast. Sounds like a great trip.

It is fast-paced but doable. If you can return the car in Split, you can work in Hvar on the way to Dubrovnik because you don’t need 3 nights to see compact Dubrovnik.
Split to Hvar Town on the Krilo catamaran takes just 1 hour. You can hike to the castle above the town, swim at Bonj/Amfora Beach and overnight in Hvar Town.
The next morning, take the 70-minute Krilo Catamaran from Hvar Town to Korcula Town. Explore tiny Korcula Town in a couple hours before continuing on to Dubrovnik by boat (2 hrs) for your final two nights. Kaleta luggage storage is right by the boat dock in Korcula Town.
www.CroatiaFerries.com has boat schedules and fares.

If you want Pltivice, then I think this itinerary works best. If you wanted more coast time, then I would consider flying in/out of Dubrovnik or Split and doing a loop (mainland and via islands).
With that full last day in Dubrovnik, you could move one of the days -- it is tiny and it does does take long to see the town. You could add a day to Split and do an island day trip (Brac or Hvar), or you could take a catamaran between Split and Dubrovnik and stop over on Korcula for a night. Or, drive up the coast and stop at Makarska for hiking (or Omis for rafting).
I am active myself, and I would rather have time on an island versus time in Dubrovnik (*I started my honeymoon there so I have a special place in my heart for it, but as pretty as it is, it gets so crowded--and I just love the islands more). I feel like it is easier to do activities like hiking, swimming, bicycling, kayaking, etc. when you are on an island versus from the cities. But I would look into kayaking while you are in Dubrovnik--I wish I had done that.

One way car rentals are great for leisurely trips where they pay off on the side trips and exploring. But you are doing direct hard drives. I would use the bus (very cheap) or a private driver (maybe not much more than your rental because of the drop off charge).

Have you checked flights because I do not believe there are any direct flights from Greece (Athens?) to Zagreb. There are direct flights to Dubrovnik though.
Therefore, I would fly into Dubrovnik, ferry to either Hvar or Korčula, ferry to Split then fly home from Split. You could visit Krka National Park from Split. Not the same but just as beautiful.
Personally, for me, the crowds at Plitvice does not make for a nice, relaxed visit. We haven’t visited there since 1978 when we practically had the lakes to ourselves, and we visit Croatia every year.

Barbara’s itinerary above is the exact one my Croatian neighbor recommended to me years ago. It turned out to be one of the best itineraries ever.
Anywhere.

Looks solid. Just drop the car in Split and take the catamaran to Dubrovnik. Late June is great, actually pre-peak season.

Thanks everyone! I realize wasn't clear in my original post, we arrive in Croatia on July 5th. I like kenko and valadeplhia's idea to add Hvar/Korcula in between Split and Dubrovnik, and I'll consider Barbara's idea of flying into Dubrovnik and out of Split if I can make the ticket change and if we decide to skip Plitvice Lakes.

Has anyone tried going early (7:30-8am) to Plitvice Lakes and heading out after lunch--the strategy many, including RS guidebook mention? It seems a shame to let the crowds scare us off from visiting when it's unlikely we'll make it back to the area for many years, if ever.

My visit to Plitvice was too long ago to advise, but your plan to see it in later afternoon/early evening and then next morning is what I most often see recommended. I would use their website to scope out the trails and have your plan.