I have no experience traveling to Europe in late fall so can't comment on what weather conditions may be like or which of your destinations--if any--may be pretty much dead at that time of year. You should definitely do so some research on wunderground.com. I had one chilly, extremely wet day in Zagreb in the second week of October 2015. Of the places you list, the only ones I know have significant indoor (weather-proof) sights are Zagreb, Ljubljana, Split and the caves.
It will help if you have a rental car so you aren't exposed to the weather waiting on buses. Train service is fairly limited in Slovenia and Croatia. Also, I'm afraid some of the buses available in the summer may not be running in November and December. Perhaps I'm being unduly pessimistic. If you are considering a rental car, be aware that you'll probably be subject to a very high drop charge if you rent the car in Croatia and drop it in Slovenia
Plitvice Lakes National Park is wonderful in good weather. I, myself, wouldn't want to be there if it was significantly wet. The walkways have no railings. Some are wooden but others are along the ground and might be covered with wet (slippery) leaves. If no one here can report on a first-hand experience, I suggest checking TripAdvisor or Googling. I haven't been to Krka National Park. I suggest that you check on that one, too.
Bled can be visited from a base in Ljubljana even if you don't have a car. Bohinj was manageable in the summer, but I don't know about frequency of bus service later in tne year. A taxi from Bled might not be exorbitant. I suspect anywhere beyond Bohinj will require a car.
The caves are viable day-trips via bus from Ljubljana in the summertime. I'd pick one or the other rather than spending the time needed to see bothPostojna and Skocjan. Skocjan is a more natural experience, without colored lights. I was 63 when I visited there, and all the formations looked pretty much the same color to me, though the guide mentioned different colors. I assume that is not an issue for people with younger eyes.
With--I assume--crowds not being a concern, Plitvice could be a day-trip from Zagreb or Split (assuming availability of transportation), but you'd be traveling to and from the park in the dark.