Itinerary advice/too much time on the islands?

I think four is the bare minimum I would devote to the islands in September, but I prioritize outdoor activities. If you are less interested in that kind of thing, then you need to spell out what you want to see and do. There are things to fill the time to be sure—farm tours, churches, pretty villages, but it is the gorgeous land and sea that really stands out on the Croatian coast.
I would only insert Plitvice if I was flying out to Zagreb and could stop en route rather than having to backtrack to Split. Istria is a different trip entirely.
I’d move one of those days in Dubrovnik to one of the islands if anything.

Mostar and Sarajevo are not day trips from Croatia. The Bay of Kotor is doable as a day trip from Dubrovnik.
I wouldn’t spend more than two nights in Split which you should see at the end of your stay.

6 nights in Dubrovnik might be too many. I would add one night to each Island. We haven’t been to Hvar, but have visited Korčula over a dozen times. We have cousins who live there.
Korčula offers lovely walks, many water activities, very smallboat taxis to neighboring islands for a day of swimming, wineries, cycling, and just relaxing lunches along the town wall with Sea views. Croatians eat their main meal around 2-3:00. All the friends we take there to visit tell us it was their favorite part of the trip.
Hvar could be just as nice.

Yes, I think you can and should rearrange things a little bit. Even with day trips 6 nights is Dubrovnik is too many. I’d keep it at 4, 5 if you’re really set on a bunch of big day trips. 2 nights in Split at the start is plenty. I suppose that puts Krka on your first full day, but I’d still do it. Split is pretty cool, but you can see it pretty well in the off-hours during your stay (including last day.) All the old palace sights sound like a lot of sightseeing, but in reality it takes under 30min to see everything.

That’s 2-3 easy nights to throw back towards the islands. I’d add one to each so you have three nights in each place. If you chose 4 nights in one place, I’m not qualified to pick one over the other but Korcula has a nice little wine country thing nearby that makes for a nice day. You can rent bikes and it’s an easy ride.

Everyone is going to have a different idea based on what they enjoy; and all the ideas are great.

I would start in Split. 2 nights each in Korcuka and Hvar or 3 nights in just one of the two is more my style. I would fly home from either Sarajevo or Podgorica or Tivat and use 3 of the Dubrovnik nights in either Bosnia or in Montenegro. If it's too late to change flights then 2 nights in Mostar or 3 nights in Perast/Kotor/Tivat then back tobDubrovnik for a night.

We did a 3 week trip to Croatia/Bosnia Herzegovina/Montenegro(Kotor)/Slovenia in May, it was lovely.

We typically have a "3 night rule" where we try to stay at least 3 nights in a place to avoid too much travel. However we broke that rule for Dubrovnik (2 nights) and felt that was fine. Walking the walls, seeing the old town, visiting a couple of museums, having some good meals, we felt that the timing was right.

For your day trips from Dubrovnik, be aware that the border crossings can be lengthy. Our 2 hour bus ride from Dubrovnik to Kotor ended up being 4 1/2 hours. We arranged a private transfer for the trip back from Kotor to Dubrovnik (which went through a quieter border crossing than the bus) in order to be sure to make our catamaran for Korcula. Although the private transfer company chose our pick up time, our driver was very stressed about making the catamaran (we made it with about 15 minutes to spare).

Similarly, our bus trip from Mostar to Dubrovnik ran about 2 hours late.

We spent 3 nights in Korcula, and although it was my favorite spot ambiance wise, we were looking for things to do on the second full day. We ended up spontaneously taking a day trip to Hvar town by ferry since that wasn't on our itinerary. Hvar town wasn't our favorite place, but we met 2 separate couples who raved about staying in Stari Grad over Hvar town.

We rented a car in Split and drove to Plitvice in the morning, saw the park in the afternoon, and spent the night at one of the hotels at the park. Plitvice is unique and I am very glad that we went. There was quite a bit of road construction, but otherwise the drive was very pleasant. The next morning we drove to Rovinj in Istria. Rovinj was lovely with its Italian history and we enjoyed day trips to the hill towns and Pula to see the coliseum.

Summarizing:

• We felt 2 nights in Dubrovnik were adequate for us to see the main sights.
• Think about whether day trips to Kotor or Mostar from Dubrovnik via public transport would be worth it (maybe do an overnight or private transportation).
• 2 nights in Korcula and 2 nights on Hvar island should be adequate unless you really want to slow down and enjoy the ambiance (for us better in Korcula than Hvar Town).
• Dubrovnik, Kotor, Korcula, Hvar, Split and even Rovinj were all variations on a theme, ancient cities on the Dalmatian Coast. We enjoyed all of them, but by the time we were done, we were ready for the change of pace that was Slovenia.