Zagreb has a beautiful, bi-level historic district and an active café-culture. If you have some moderate weather, you will enjoy walking around. There are also a lot of good art musuems. There are some quite small ones that are single-artist, but my favorite was the Naïve Art Musuem. It's only a few rooms but it's a fine collection. It's on the second floor of a building in the old town, and I don't think there is an elevator.
There are some large museums positioned more or less between the old town and the train station. Keep an eye out for announcements about special exhibitions. I was lucky enough to catch a very nice Rodin exhibition during my 2015 trip.
Ljubljana is a charming city; it's about 2-1/2 hours from Zabreb by train or bus. ViaMichelin gives a driving-time estimate of 1 hr. 43, but I don't know how much extra time you'd need for retrieving the car in Zagreb and parking it in Ljubljana. Ljubljana is definitely worth a night or two, though.
For Plitvice Lakes, ViaMichelin estimates about 2-1/2 hours one way. Part of the drive is along what I'd call a "two-lane country road", and I have no idea how reliable VM's estimate is. You'll want a nice day for Plitvice; part of the time you'll be walking on unpaved paths that might be covered with slippery leaves. If the weather is great on a weekend, you might have to contend with a spike in Croatian visitors, so I'd tend to favor making the Plitvice trip on a weekday. I'm hoping that, since your trip is so far off-season, you won't experience the dreadful mid-day crowding we warn people about.
I experienced a raw, wet day in Zagreb in mid-October at the end of my last trip to that area, so I definitely recommend layers and good rain protection.
