I doubt it would be hard to find a place without a 3 night minimum in late September in Hvar.
Only probably with the latest itinerary is the long day of driving from Zagreb to Plitvice to Trogir. I know it's also not ideal to fly into Zagreb and immediately rent a car and drive, but I'd probably recommend that if possible. The reason is that you could get up first thing the next morning and see the park before it gets crowded. If you have to rent the car the next morning in Zagreb, you might not get down to the park (about a two hour drive) until well after noon. I have heard more than one complaint about Plitvice being too crowded from people who didn't get there til later - there may be lines of people and a crowded, Disneyland-like feel. Earlier in the morning it is not crowded.
The drive from Zagreb to Plitvice is not difficult. If you think you could manage it after the long flight, consider staying in one of the overpriced park hotels so you can walk right into the park the next morning.
I haven't been to Hvar (only to Korcula). I have also been to Zadar, which was OK but not my favorite. I liked Trogir a little more, but it's a very small town - a great place to relax, but unless you have day trips planned I wouldn't expect to want to spend two nights there. I'd probably go to Zadar after Plitvice if you really want to see Zadar instead of two nights in Trogir. (Note that parking close-in in Zadar can be a challenge - most of the center is a big pedestrian area. I don't remember what the parking lot situation was; I was very lucky my B&B owner found me the PERFECT free parking spot - out of only four right in that area! - a short walk from my B&B.)
Mostar vs. Kotor: yes, comparing the two towns, Mostar is a more historically interesting and significant city. But if you are interested in great scenery, I'd go to Kotor hands down. The Bay of Kotor has breathtaking scenery, and the views down from "walking the walls" above Kotor are amazing. Kotor itself was OK - not a city I fell in love with, but for me the amazing scenery made my brief visit well worth it. I did both Mostar and Kotor as overnights not day trips, though. Both will be crowded mid-day with tour groups (and cruise ship groups in Kotor, the same people who were in Dubrovnik the previous night or the next night). Mostar just get bus tour groups. I also did a twisty drive above Kotor through the mountains on a drive to the town of Cetinje - with unbelievable eye-popping views down on the bay; this might be make for a very long day of driving as a day trip from Dubrovnik, although this is what Rick Steves recommends.
The drive to Mostar isn't really scenic at all, nor is there a view down from anywhere. The rebuilt Stari Most (old bridge) in the center of town is quite amazing, though, and seeing a part Muslim city with mosques etc. makes for a nice contrast from everything else you've seen in Croatia. Kotor doesn't feel that different.
I think if I were to wake up in the morning in Dubrovnik and find it rainy, I'd drive to Mostar; if the weather was beautiful, I'd drive to Kotor, because I love scenic photography, and Mostar would be just as interesting in the rain.