With 2 weeks you can do quite a bit, but you can't do it all.
If you hope for a bit of city culture, I'll put in a plug for Zagreb. It has a very nice bi-level historic district and a lot of very enjoyable museums. There are quite a few art museums (some single-artist places), plus two quirky options I especially enjoyed: the Museum of Naïve Art (small but stunning) and the Museum of Broken Relationships. If you fly into Zagreb, remember that your arrival day may not be good for much beyond aimless wandering around outdoors, trying to stay awake.
With 2 weeks I would consider Plitvice pretty much mandatory (and I seldom put places in that category). The trick is to spend the night before your visit in or very near the park so you can get inside when it opens. A midday visit will find the park grotesquely crowded. You could also try to arrive mid- to late-afternoon and see part of the park then, finishing up the next morning. It's a glorious place, but you simply must time it right. The park has recently started selling online tickets in advance for specific time-slots, and you are not guaranteed to get in if you don't have one of those tickets.
I think Istria benefits from 4 nights. There are a lot of nice towns and villages to enjoy (Rovinj, Porec, tiny Vrsar, Pula, Motovun, Groznjan), and the inland scenery is very nice. I think 3 nights (giving you just 2 full days) would be rather challenging. This is assuming you'd have a car in that area. As of 2015 the only way for those without cars to see both Motovun and Groznjan on a single day was to take a bus tour called "Inland Istria" that operated only on Wednesdays. So I think from a time standpoint you kind of have to choose between Istria and side-trips outside Croatia, assuming you want to get to an island or two.
I love Ljubljana, but to me it's a bit too far away and has a bit too much to offer to try to make it a day-trip.
Montenegro is a beautiful country, but the national parks seem not to be accessible by public transportation. If you're driving, you'll have that option. There are many very interesting towns, some not overwhelmed by tourists, but I think you'll find two weeks isn't really long enough to do a good job of seeing Croatia and also see much of Montenegro.
I liked the less-touristy Herceg-Novi, the Turkish-feeling Ulcinj, the old capital of Cetinje and the more-touristy (disastrously so if a mega-ship is in port) Kotor. The drive around the Bay of Kotor is one of Europe's great natural sights. I think it is a fair comment, though, that Kotor is sort of a mini-Dubrovnik. I appreciated the two places more for having visited them on two different trips.
Bosnia-Hercegovina is also a good side-jaunt from southern Croatia, but again, there's the issue of time. Mostar is the most common destination. With more time you could do a multi-day loop and include Sarajevo as well. I know at least one person on the forum has commented positively on Trebinje.
If you rent a car you'll need to advise the company of borders you plan to cross and get permission in advance. There may be insurance issues. Even just going to Dubrovnik requires crossing a bit of Bosnia-Hercegovina.
