Hvar, Korcula, Split, Dubrovnik - beaches/lodging/transportation?

You will have 3 full days in Croatia. Every time you move from one place to another, you will consume mush (maybe most) of that day (yes, if you are very efficient, and the logistics work out perfectly, it may take you just a few hours to make the actual move, but getting checked out, getting to your transport, finding your way upon arrival, getting checked in, getting oriented, etc.) adds up.

I think you need to be more realistic about how many locations you can reasonably cover.

You arrive in Split and you depart from Dubrovnik. With just 3 days, I'd pick just one other intermediate destination (personally, I loved Korcula and disliked Hvar, but tastes vary). I'd suggest you try not to cram in much more than that.

Sorry, I should have said I don't need to go to al of those but am flying into Split and out of Dubrovnik.

I haven't been to any of the Croatian islands recently, but others here have said that many of the island lodgings have 3-night minimums. If that is the case, you may be limited to doing a day-trip to an island, in which case I would select carefully, considering the length of the ferry journey.

I hope some folks here can make a few suggestions.

Given your preference for less big cities, miss out Split and go to Hvar. You talk about must-sees. As you are going to Dubrovnik, it would be odd to ignore it.

I would do two nights in Stari Grad on Hvar, and two nights in Cavtat near to Dubrovnik airport. There are frequent ferries from Split to Stari Grad. Cavtat provides easy access to Dubrovnik by bus or water taxi, but is far less crowded than Dubrovnik itself. From Cavtat you are a 10 minute taxi ride from the airport.

If you don't want to see the major sites, it begs the question why bother going there, especially as you don't really have time to see much once you disregard all the travel time. Why not just go to Greece for longer? Croatia to Greece - there aren't many good travel connections.

It seems such a shame not to see Trogir, Split and Dubrovnik, but that's about all you would have time to cover.

What time do you arrive at Split airport? Arriving there at 9.30 am usually means c 4 pm at my accommodation on Hvar when I have travelled there.

Assuming you arrive early at Split - with your timescale, I would suggest that you stay on the mainland - somewhere such as Omis would suit. Go to Dubrovnik for your last night and explore the city.

My husband and I are planning about a week in Croatia in September so have done a lot of research about this. We are only spending one day in Split and one in Dubrovnik as we did not want to miss either city but want to spend most of the time in the islands. We were able to get a room for 2 nights in Korcula so not exactly correct about having to book for 3 night minimum. I guess it might be that way in peak season? We then booked for 3 nights on Bol ( Brac island). We are not late night party people so avoided Hvar as we read that is where the action is and read so much about how beautiful Brac was that we decided to go there. Make sure you check out the cruise ship schedule when in Dubrovnik and avoid those days or at least the Old Town on those days. I did this and found the day we were planning on visiting there was going to be over 6,000 people so rearranged our schedule to miss that day!!

Depending upon you arrival time, you could depart Split for an island the day you arrive. If you have some time to kill in Split, you can store luggage at the port and walk around Diocletian's palace.
For your island transport options, see http://www.krilo.hr/en/ and http://www.jadrolinija.hr/. Note also that a bus goes from Korcula to Dubrovnik (bus takes ferry).
I would choose either Vis (since you mentioned renting scooters--it's great for that, with some fantastic beaches), Hvar (but not Hvar town in July, instead the more sedate Stari Grad), or Korcula. Assuming you will spend your last night in Dubrovnik and do not wish to spend a night in Split, that leaves you 3 nights to play with. I think 3 in one place would be vastly superior to 2 and 1 (on two different islands), but your call. Start looking at accommodations soon--I think you can find something for less than 3 nights, you just might pay a surcharge.

Thank you all. I think we decided it would be best to do Greece at a later time and just focus most of our time in Croatia from July 9-19. We'll either start out in Dubrovnik and work our way north or start out in Ljubljana and work our way south. I just need to figure out if we're flying or taking train - will depend on where we can get cheapest flight back to states. This will give us a mix of nature, history, small towns with slight stop in cities, and time near the sea. Economical accommodation recommendations welcome. Thanks for your input.

I think that's a fine idea. Both countries have so many great destinations.

I flew back to the US from Zagreb in 2015. It worked well, but Washington DC is pretty easy to get to. I don't know what sort of connections will be necessary if you depart from Dubrovnik or Ljubljana. I guess you might try Split as well.

Thank you all. I think we decided it would be best to do Greece at a later time and just focus most of our time in Croatia from July 9-19. We'll either start out in Dubrovnik and work our way north or start out in Ljubljana and work our way south. I just need to figure out if we're flying or taking train - will depend on where we can get cheapest flight back to states. This will give us a mix of nature, history, small towns with slight stop in cities, and time near the sea. Economical accommodation recommendations welcome. Thanks for your input.

As you search for flights, you might consider reducing the scope. Ljubljana to Dubrovnik is quite a bit of travel for 10 days.
It is easy to rent apartments in Croatia, and the tourism websites of most towns/islands have accommodation links.