Travel from Vienna to Croatia assistance needed

Check the Deutsche Bahn website. They don't have schedule for September yet so I checked the December schedule. They have several trains with at least one change. It takes at least 15 hours altogether. You change trains in Zagreb. Arrive in Split in the morning. In September there is still season so let's hope there will be a direct sleeper train to Split.
Or you can fly 2 hours 20 minutes with one stop in Zagreb.

Take the train from Vienna to Zagreb and then rent a car. Croatia's public transportation system is limited and tedious; the roads and car ferries are excellent.

Use www.oebb.at for train tickets and schedules.

I did not have the same experience as the prior poster. Between Split and Dubrovnik (where there is no train service), I found the bus system very easy to use and not at all cumbersome. Nice, new, clean and modern buses ran up and down the coast regularly. And much cheaper than renting a car, which would have been a pain to deal with on the islands (I simply didn't need it on the islands, everything was walkable or one could rent a scooter for the day).

A train ride from Vienna to Zagreb will take twice as long as a flight - I would opt to fly.

The schedule only extends to early April at this point, but Flixbus has two daytime buses running from Vienna to Zagreb. Travel time is 5 hours. It's possible that other companies offer service, too.

Zagreb is quite a nice city. It has a pretty, multi-level old town and a lot of museums. The museum of naïve art is small but very worthwhile, and there are a number of more mainstream museums as well.

Eurowings, non stop, one hour, $64 Vienna to Zadar. Then its less than 2 hours to Plitvice and less than 2 hours to Split (opposite direction)

Train Vienna to Zagreb, 1 change, I am going to guess about the same price as the flight, but about 9 hours, then less than 2 hours to Plitvice followed by something less than 3 hours or so to Split.

No exactly accurate advice above. There are direct trains from Vienna to Zagreb taking a bit under 7 hours. I stand by the car rental suggestion - it is the easiest way to explore the nooks and crannies.

I also much prefer the coast to Zagreb. Zadar is a lovely city and a great gateway, so if you can get that cheap flight - go for it. Flights to Split are also reasonable.

Thanks for all the helpful advice. We are looking into flights vs trains and train from Vienna to Split takes 15 hrs and cost 136 euro each. Only direct flight I could find was through Croatia Air only takes 1hr20 min but cost 337 US dollars but the time saved might be worth the cost, though I will definitely look into the Eurowings flight to Zadar. Just looked up where Zadar is and we might just do that and skip Plitvice and do Krka instead since it is much closer (realize I should be talking about this in the Croatia forum but you folks are so knowledgeable I will mention here as well to get more feedback).
Thanks so much fot the great feedback!

Only direct flight I could find was through Croatia Air only takes 1hr20 min but cost 337 US dollars

I would wait....September 2017 is a long way out. This price may come down by then, it's not static.

I'm surprised there are virtually no cheap flight options to Zagreb, Zadar or Split. I thought flights were usually bookable 11 or 12 months out, but perhaps some of the September schedules just haven't been loaded yet. I'd be taking the bus, that's for sure.

Zadar is very nice; the old town is charming and it has two interesting contemporary monuments on the waterfront. I like Zagreb a lot, and it has more to see and do than Zadar. I admit, though, that Zadar is more different from what you might have seen while in Austria.

I haven't been to Krka so can't compare it to Plitvice. I'm sure it's much, much less crowded. One great thing about Plitvice--if you can avoid the crowds--is that it has an extensive system of trails winding around the small lakes and waterfalls. I do not know whether Krka compares in that regard. I am a bit doubtful, but I haven't gone out of my way to research Krka.

CHEAP FLIGHTS
Many of the discount airlines don't post routes and fares more than 6 months in advance, so there may be others shown between now and March or April. I did a quick look on Google Flights for the week of September 10th and found the Eurowings flights on Sunday, Wednesday and Saturday. Direct, non-stop 1:05 flight time. $65.

https://www.google.com/flights/#search;f=VIE,XWW;t=ZAD;d=2017-09-10;r=2017-09-20;tt=o;s=0;mc=m

Also, Vienna is a pretty crummy hub for discount airline connections. For that you want Budapest or Belgrade.

I am in Croatia most Septembers, and I use the Deutsche Bahn website to book my train tickets. I usually fly to Zagreb, which is as noted a very interesting city now (recently voted best capital in Europe to spend Advent/Christmas in, for the second year running) and after my time around Croatia I return by train to Munich via Salzburg. You can do the route in reverse, obviously, so you could change in Salzburg to go to Zagreb. The stretch between Zagreb and Salzburg goes through some wonderful Slovenian and Austrian alpine valleys, and I usually sit in the restaurant car for the best bits for the big windows and something to eat. If you are travelling back to Germany, there is an Europa-Spezial Ticket which is hugely discounted for any route into German , as a promotion. There may be similar deals on the Austrian OBB website. I travel first class, which is not much more, and usually have a compartment to myself, as few people can get this price break or want to travel by train if they can afford to fly. I love my train day. Trains from Zagreb to Split are new and high speed. So is the bus on the new Autoput freeway. Zadar is a true gem, especially in September, and can be reached as noted by Croatia Airlines turboprop every day from Zagreb. But you would miss seeing Croatia en route. In years of going to Croatia I have never been to Plitvice, the coast and the capital have so much to see and do. Especially any island you like.
Bus travel in Croatia is clean and comfortable and cheap. Autotrans.hr has schedules and a UK flag icon switches it all to English.
As noted, Vienna is not a hub for cheap flights. Germany is full of them, still running until the end of September. See Kayak for ideas. You could fly to Split or Zadar and wander back by bus and train.