Croatia And other countries for 14-15 days

Impossible to answer the flight question for you--get started by searching on Kayak or whatever search engine you like. I am able to get to Croatia with one stop from the east coast. Open jaw/multi city is best because the country is long and skinny, so I like a north to south (or vice versa) plan. Of course if Zagreb works out better price- and schedule-wise, then no biggie.
Do you want to drive or stick to public transport (or both, as needed)?
With two weeks, you can basically do it all--Istria, with a jaunt into Slovenia if desired, the Zagreb area, and Dalmatia--even an island. You can also visit Bosnia and Montenegro. I'd start by nailing down the places you want to see. I will recommend a visit to Plitvice lakes national park, even though you have hikes/nature at home, it is a unique place.
Depending on your wish list, you will probably have to move more than three times. Given the geography and such, it just sometimes makes more sense to move more -- and that is sometimes preferable to really long day trips.
A rough sketch would look like this, but of course this will evolve based on YOUR interests and the flights that work out best.
Zagreb 2 nights
Plitvice 1 night
Split 4-5 days if you want to do day trips
Hvar or another island ~3 days
Dubrovnik 3 days
Any of the above could be replaced with a side trip to Bosnia or Montenegro, or you could swap for Istria, etc. This is just a start to show you how it could look.

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.

I agree with acraven about including Plitvice in your itinerary. We just came from there and we are currently in Zagreb. Plitvice is amazing, beautiful, and unique, even on a cloudy day!

We stayed at the Plitvice Miric Inn, which I recommend. It’s just outside the park, about a 5-minute drive.. The included breakfast buffet is huge and delicious! We had dinner at their restaurant and it is outstanding & only costs 20 euros. We selected fresh whole trout for our entree. It came with homemade chicken soup, a fresh salad, roasted veggies, potatoes, polenta & risotto. The dessert, apple strudel, is to die for.

We ordered tickets for 4PM entry on our first day. It wasn’t too crowded. We hiked the upper lakes. On second day, we arrived at the park at 8:30am. We left the park by noon, and there were about 20 tour Buses in the parking lot. I kid you not!

I am traveling now. My international flight was Seattle to London by Icelandair. Very frugal! Then a quick hop to Venice. Pack almost nothing and in a small bag and every European country has a cheap airline, some of which don’t show up on the big search sites. And they can be under $20 flight if you catch the right moment. From Venice is a couple hours by bus to Ljubljana, which has rail service into Croatia and is a friendly entrance to Eastern Europe. Check out UNESCO sites for some stunning stuff. If you go down the Croatian coast you will find lovely city after lovely city with top sophistication and easy traveling. But I would hop over to Zagreb and afterward head west to the lovelies. Get out a map and chart a course. Buses go virtually everywhere, and trains disappear as you head south. If you get brain fog from beautiful Croatian cities just get out of Croatia. Mostar is close and easy and with a wholly different vibe. Out of Mostar is back to Dubrovnik if you decide on the good life, or Montenegro for a bit more grit. I am ending in Tirana, Albania for a cheapo flight to London and complete the Icelandair round trip. Most main city to main city buses (I.e. Zadar to Split) average $15 and 3 to 5 hours. In Croatia when you arrive at a station, ask about departure buses to places you’re thinking about. They have little handouts in English with departure times and destinations. Easy traveling and beautiful coastline. Enjoy!!

I would recommend taking Split and Dubrovnik as bases.
From Split, it's a good idea to take a day trip to Trogir, Sibenik, Krka, Klis fortress, ancient Salona, Omis and do island hopping tour. If you want, you can stay for a few days in some of the nearby islands like Hvar, Brac or Korcula.
The other time I would stay in Dubrovnik, exploring it for a few days, and taking day trips to BiH and Montenegro.

American flies direct to Dubrovnik out of Philadelphia. You can also fly back through Venice (a ferry ride from Istria). Look into an 8 day small ship cruise, 19-20 cabins. They have several routes that take you to many islands with lots of sight seeing and some go to Montenegro.