I like your plan. You can return for a second visit and hit Split/Dubrovnik/Montenegro and possibly some Bosnian sights.
I enjoyed a stop-over in Zadar on last year's trip. It's a coastal city not too far south of Istria with a very pretty old town on a peninsula. Nice for wandering. Definitely has been discovered by European tourists, though.
In Istria, I stayed in Rovinj and saw Porec on a day trip with a brief stop in Vrsar. Rovinj and Porec are physically very different, so I recommend seeing both. Vrsar is small but also worth a visit; there were very, very few tourist around on the day of my visit, which was nice. Try to get to a few of the inland towns as well; my favorites were Motovun and Groznjan. Seeing the interior is rather hard to do by public bus, but you can probably pick up a one-day bus tour if you don't want to drive and are based in one of the major coastal towns like Rovinj, Porec, or Pula. I suggest trying to get some information on that ahead of time, because the trip I took ran only one day a week. I'm sorry that I don't remember the name of the operator, but I believe the name of the tour was "Inland Istria". I had to go to three travel agencies in Rovinj before I found one that sold the trip.
I liked Zagreb a lot. The historic area is very nice for wandering or café-sitting. Most of the many museums are a short walk from the tourist district or actually in it. Ask the tourist office for its museum brochure if it's not on display. It was very helpful.
Plitvice was overrun when I was there on a late-August Friday last year. The line to buy tickets was about an hour long at 10 AM. I urge you to stay overnight in the area and get an early start on your walk. Plitvice is lovely and I consider it unmissable, but it will be much more enjoyable if you can get a jump on the day-trippers. I have no idea whether it would make much difference, but I'd try to avoid Friday-Sunday if possible. There's a comprehensive trail map for sale in the shop (not at the ticket booth). I suggest buying that so you have the option of choosing your own route if the marked loops are too crowded for your taste.