Hello! I will be on my honeymoon late September in Croatia. Between our stays in Dubrovnik and Split, we have two nights open to go out to an island. Any advice between how to choose between either Korcula or Hvar? Also, I see that there are very limited (or non existent) sailing options from Dubrovnik out to either of those islands (will be going out of Dubrovnik on a Saturday and prefer to leave Dubrovnik early in the day to get to the island.) Any advice on options of how to get to those islands from going out of Dubrovnik? One other option is I have not booked our Split hotel yet, I was avoiding going from Dubrovnik to Split and then to the islands, as I thought it would be easier to go from Dubrovnik, islands and end in Split (we fly into Dubrovnik and out of Split) - but I do know there are more sailing options out of Split. Is the extra travel time worth it to go from Dubrovnik to Split (stay in Split), go to island, sail back to Split and fly out? Once again, I was hoping to do Dubrovnik, sail to island for a couple of days, sail to Split and end with spending time there and fly out. Thank you!
The most logical route as you have suggested is Dubrovnik - island - Split. The only option to Hvar from Dubrovnik is the Krilo catamaran that leaves in the afternoon. Korcula gives you more options, as you can also take the bus there.
You don't say how many nights your trip is in total. Some island accommodation has a 3 night minimum booking, but there maybe more flexibility in late September. I'm not sure if you could snatch another night for an island from your other stays.
For stopping en route between Dubrovnik and Split, Korcula and Hvar are your best bets.
Catamaran and ferry schedules:
https://www.krilo.hr/en/
http://www.jadrolinija.hr/
Check the bus to Korcula also (bus takes a short ferry). Confirm schedules you find on this consolidator website: http://www.buscroatia.com/dubrovnik-korcula/