I was in Dubrovnik in early October the first time, but it was eight years ago. I suspect it will be busy during the day but much quieter at night; it wasn't dead when I was there but is probably busier now. Cruise ship tourists can pack the place even in October I think. You can dig up a website that lets you check cruise ship schedules to try to see how many might be in port on a particular day to avoid crowds, if you time it right.
Have you considered flying to Dubrovnik and ending in Ljubljana? The weather turns sometime in October - was mid-October when I was there, turned cold and rainy the day after I left Dubrovnik that year. The earlier you get there, the better your odds of good weather. In Ljubljana, it may not matter so much how nice the weather is, but along the coast, I'd prefer nicer weather. Obviously the weather is different year to year and you are just playing the odds...
Are you prepared for a steep one-way rental drop fee to pick up a car in Slovenia and drop it in Croatia? Could be 500 Euros just for that - FYI if you haven't checked. Alternative ways to avoid this: fly into Zagreb instead of Ljubljana (one-way rental in Croatia probably won't incur a drop fee if rented longer than four days). You could still drive to Ljubljana immediately from Zagreb, but of course that adds driving time and eats some of your short time to explore.
Alternately, you could do without a car in Slovenia and just take the train to Zagreb and rent the car there. It's also possible to rent a car just for a day in Ljubljana. You don't need a car to get up to say Lake Bled for the day - easy by bus - but there is some amazing scenery along the way if you detour by car. My favorite route is via the lovely town of Skofja Loka (worth a stop), then take the scenic detour up through the mountains via Jamnik and Kropa - gorgeous scenery looking down and some neat stops, one of of my favorite things to do in Slovenia.
Otherwise, it's not a difficult drive from Zagreb to Dubrovnik. It's mostly freeway, other than the detour to Plitvice heading south from Zagreb, then the slower coastal road you pick up about an hour north of Dubrovnik. I drove from Zagreb to Plitvice to the town of Baska Voda (south of Split) to Mostar to Dubrovnik with a night each in Plitvice, Baska Voda, and Mostar. (Doing it again, I probably would have spent the night in Sibenik or Trogir instead of Baska Voda.) Let's say you have seven nights. Then you could do:
Ljubljana (2 nights)
Plitvice (1 night)
Split (2 nights)
Dubrovnik (2 nights)
The longest drives would be between Ljubljana and Plitvice I think - and if you train to Zagreb and pick up a car, it's only about a two hour drive from Zagreb to Plitvice. Split to Dubrovnik might be 3 hours or so.
If this seems too fast of a pace, skip Ljubljana and start in Zagreb (which some people like, though I wasn't a big fan).
