December Slovenia & Croatia Route

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.

Thank you so much for your advice and sharing your experience! We will be driving so that should make things a little easier with transport.
Would you care to share your favorite experiences in Slovenia?

I missed out on some of the things I had planned to do last time around because of illness. I loved Ljubljana: the markets, the wandering around; I even found a cat cafe. Bled was lovely in the summer. On a quick trip Bohinj wasn't as picturesque as Bled (duh). Vintgar was fun but not remotely in the same category as Plitvice--a completely different experience except that both were very crowded.. I definitely recommend one of the cave systems.

You have big list. First recommendation, to rent a car, one in Croatia and one in Slovenia. Drop off charge in another country is step. Croatia seaside towns and island will be empty and dull out of season, bar main attractions as are Split, Trogir, Dubrovnik. Plitvice are fine for visit, but keep in mind short days.
Slovenia is more all year destination and here you will have more options, but still not as many as in summer. Caves are must and also Predjama Castle. You can base in Ljubljana for few days, do day trips. Most locations are short drive away. Check weather reports, in higher places could be snow - Velika Planina, Vogel etc. Logar valley you must do Panoramic Road and if there are no snow you can go by Pavlic Pass to Austria and back over Jezersko to Slovenia. Very scenic route.
Only Soca Valley is too far from Ljubljana for day trip, so base yourself for two nights and explore Kobarid, Source of Soca etc. Visit TIC and they will give you all sort of informations on the region. For Zip Line look at http://en.ziplineslovenia.si/

Forgot to add that Ljubljana Christmas Market is something special and Zagreb is also very nice. Food scene in Ljubljana is shocking and if you are for fine dining visit Hisa Franko in Kobarid.

We visited lake bled in the summer. Im pretty sure the plinkas/rowboats across the lake shut down in the fall...however you could drive up the hill to the castle.... it had an impressive museum, and there we had my favorite meal of the whole trip..... but part of it was the amazing views. We stayed at mulej bled turist farm, which i recommend

@astiskovski sorry did you mean Logar Valley is a must do? Or Panaromic Pass?
Thanks!

All are basically in Logar Valley and are main attraction. Visit some Tourist farm for really nice, delicious food.