I dont think we were a lot of help. So some more thoughts.
Given the time you have skip Mostar.
More of what you seem to be looking for exists in Montenegro than anywhere you mentioned. Watch the videos here: https://community.ricksteves.com/travel-forum/montenegro/podgorica-to-dubrovnik-by-car
And since you have limited time, I think a travel planner will make a difference in this region especially because transportation isnt as easy as it is in Western Europe so knowing the options and how to piece it together does help. There is a travel planner referenced in that other thread (above) as well. I know she does Montenegro and Croatia, but not sure about Slovenia.
You said:
Things we like:
Nature - trail walks and easy to moderate hikes in lake, mountain and coastal areas
Not much of that in Ljubljana, Zagreb, Split, Dubrovnik, Budva
Hikes and Trail Walks: Perast, Kotor, Stari Bar, Ulcinj, Žabljak / Tara Canyon. Nature: Žabljak / Tara Canyon
Viewpoints
Good: Bled, Perast, Ulcinj, Žabljak/Tara Canyon, Ostrog, P1 Highway
Quaint villages
Some between stops the full length of the trip. Stari Bar comes to mind. But again, this is where a travel planner can help.
Historical sites, especially "cradle of civilization" and ancient sites
Not much ancient in the region. Close as you get is Split but not much context left there.
Things we DON'T like or care about:
lots of people/touristy
Croatia is about as touristy as life gets. Montenegro is the opposite and Slovenia probably fall in the middle (my impression at least)
great food (we have a lot of dietary restrictions so it's usually wasted on us)
Then you won’t be disappointed in Croatia. Never had a great meal there in there trips. Best meal in the region was after a fishing trip. The captain of the boat gave us directions in town (Budva) where to go with the catch and have it prepared. Excellent meal.
shopping, nightlife
Again, you wont be disappointed. Well, Split might be a pain for you. Lots of drunk trust fund brats
lounging on the beach
There is that in Croatia and Montenegro. I’m not into it much either but the off-coast fishing and water sports I enjoy.