Croatia/Slovenia/Montenegro

I think with only 14 days you are going to have to do some trimming. I sort of like Budapest, but i don't think it fits with the rest of the schedule.

My experience is limited to Dubrovnik to Titograd; so I can't help you with an itinerary. But I can tell you what I enjoyed.

Dubrovnik: Two nights. Arrive late one day, spend the night and the next night an then move on. Its stunning, especially in the evening. But its a pure tourist venue. Not much real about it any longer.

Herceg-Novi: a fascinating and beautiful old city, now a big Russian tourist spot. Spent the day and would return for a night or two in a heart beat. Actually, I am returning for a night in a few weeks.

Perast: Probably one of the more magical places i have ever visited. Sitting on the bay front as the sun set watching a tall ship pass by...... Our Lady of the Rocks and St. George ..... I will be back.....

Kotor: a smaller less impressive, just as crowded version Dubrovnik.

The impossible road over the mountain to Cetinje: Again and again and again. The road, along with the Prosciutto towards the top, is more than worth the time.

Cetinje: naaaaaaa

Titograd (Podgorica): I call it Titograd because it has all the charm an beauty of a place named Titograd (none), what it does have is a dang good airport with direct service to Belgrade and Budapest and Rome......

Budva and Ulcinj on the coast and Žabljak, the Tara River Canyon and Mojkovac are places on our list in few weeks. Just do google images and see why.

Hmmm. After reading that I will need to re-think 7 nights in dubrovnik - I do not like touristy things.jet

Some of the catamarans run year round, weather-permitting. The one between Split and Hvar does run year round, but it won't run if the seas are stormy.

With two weeks, I suggest you limit yourself either to Slovenia and northern Croatia - or the south - Dalmatian coast and Montenegro. End of September isn't a bad time to be on the Dalmatian coast but the season will begin to change sometime in October and things start to shut down for the season after September. The islands may seem pretty dead by October - I know Korcula was when I visited in early October. On the upside, you'll find fewer tourists at that time of year.

If you do the north: Ljubljana, Lake Bled, Julian Alps loop, Triglav National Park, Piran, Croatian Istria, Plitvice Lakes National Park, Zagreb.

If you do the south: Zadar, Sibenik, Krka National Park, Split, Hvar or Korcula, Dubrovnik, Montenegro. You could perhaps start in Zagreb and stop in Plitvice, depending on how much time you want to spend in Montenegro. Actually, in that case, I'd try to start in south and work my way north to Plitvice, as the season winds down on the coast.

There are a number of well marketed day trips out of Dubrovnik that might help stretch the time. We did Dubrovnik and did enjoy the 2 nights but recognized we had planned well and that was the limit. But only our opinion so ask around. From Dubrovnik we drove down the coast and spent a couple of nights in Perast on the Bay of Kotor before going on to Podgorica and a flight to Budapest.

Montenegro so impressive that we are heading back for a week in September. Half on the coast and half in the mountains. Fishing among other things in both locals. At the end flying on to Budapest nonstop for about $100. Part of the beauty of Montenegro is the cost. A full time private guide, car, driver and a nice room can be about $200 a day in Montenegro.

So, you will be in Zurich, but have two weeks to spend outside of Zurich, returning there before your flight home--correct?
I would start by look at all of your flight options. I agree to choose Slovenia and northern Croatia or southern Croatia and Montenegro.
Budapest is a bit of an outlier, but there are convenient trains from Ljubljana and Zagreb.

Prague is also an outlier. If you fly to Prague, then you need another flight south, since it takes 11-12 hours by train or bus to get just as far as Ljubljana. Budapest is actually a faster train route, with a direct, 8-hour train departing at 8:30 a.m. to Ljubljana or a direct afternoon departure to Zagreb at only 6.25 hours.

Transport connections make Croatia not as easy to slot into another trip as you might think, so try to make the most of it, if it's your destination this time.

Explore flights at www.skyscanner.com and trains through the Deutsche Bahn link at Looking Up Train Schedules and Routes Online.

Yes we will need to fly back to Zurich.

Thanks for everyone's help.

Since got to and from Zurich is the one stationary requirement I suggest you search by flights. I like Google Flights cause I can search Zurich to Europe and see all the possibilities plotted out on a map. Searching Zurich to Europe for Sat, Sep 30, I get
Zagreb ($137), Belgrade ($147), Ljubljana ($267), Sofia ($144), Split ($327), Dubrovnik ($294), Podgorica (Titograd $235), Skopje ($212), Sarajevo ($193), Pristina ($213), Nis ($102), Budapest ($228), Prague ($88)
https://www.google.com/flights/?hl=en&f=0&gl=us#search;f=ZRH,ZLP;t=r-Europe-0x46ed8886cfadda85%253A0x72ef99e6b3fcf079;d=2017-09-30;r=2017-10-04;tt=o;s=0;mc=m

So just a wild idea would be Zurich to Podgorica (spend 4 nights in Montenegro), then up the coast to Ljubliana (2 nights), then bus to Zagreb (4 more nights with some day tours). Then fly Zagreb to Prague (4 more nights, $95 nonstop), then fly Prague to Zurich on another nonstop for about $100. But you have to coordinate the cities with the dates you travel because not every connection is served every day.