AM...my son was in Croatia and Slovenia earlier this year. He jumped his cruise ship a day early and with friends rented a car so they could tour the region more extensively! I was interested in his reports because I travelled that area pretty intensively when it was all the former nation of Yugoslavia.
Anyway, my son reported positively about the whole experience. Definitely put Split on your itinerary (Diocletian's Palace is worth half a day) and you could also take a side trip to Trogir just up the coast from Split. From Split you will also want to travel south to Dubrovnik...a sort of land version of Venice! As "Ragusa" it was part of the Venetian empire and many of its buildings are reminiscent of Venetian architecture. You might also want to venture out to the islands off the Dalmatian Coast (Hvar and Korcula are the biggest) and make them part of your stay. OK...that's just Croatia. September is perfect there for weather, by the way. Not too hot but still warm enough to enjoy swimming in the Adriatic.
You could investigate travelling further south into Montenegro (Crna Gora) which is also independent. The coast line is breathtaking from both the sea and by road (not the best roads and beware of the drivers) and the various towns (Budva, Sveti Stefan) all have something of interest or beauty. You will want to taste the wines!
I've been to both Vienna and Prague. Both are big touristy cities with lots of city type tourism so you could "do" those then head over to the Adriatic Coast for a change.
By the way, I am a big fan of Lonely Planet, both their guidebooks and their website. Google them and start reading. They cater more for the adventurer.
Re using a travel agent and with all due respect to travel agents, my experience with them has not been positive in recent years. Most of them only want to sell you a land package or a cruise to places they don't know first hand. I questioned my neighbour (who IS a travel agent) about this and she confirmed as much. They earn based on commission and they don't make commission on Croatian railway tickets!