In September we are going to the Dolomites through Bolzano and then heading over to Ljubljana. I know the train schedules are not posted that far out but I've checked the Deutsche Bahn site to get some kind of idea for planning purposes. It has trains heading north out of Bolzano to Fortrezza to Lienz, Austria to Villach, Austria and down to Ljubljana with the shortest times in the 8 to 8.5 hour zone. The other alternative is to go south out of Bolzano and over to Trieste (5 to 6 hours) and take a bus or GoOpti to Ljubljana. Is that the better choice or is there a third option?
Trieste is an option. Have you considered a train from Bolzano to Venice >GoOpti> Ljubljana? See Rome2rio site for train service. May be shorter distance? We took a shared GoOpti van from Venice>Ljubljana. It was affordable, on time, comfortable, and we were dropped off near train station. It was a short easy walk to town.
You appear to have the main choices correctly identified. You are going around the Dolomite Alps and the Julian Alps... One can go across on local buses for a fun and scenic set of rides but I doubt if you would save time.
I see the 7:02 departure from Bolzano as taking 7 1/2 hours going via Lienz and Villach. That includes a 49 minute train change in Villach.
I see the 7:12 departure from Bolzano as taking 5 hours to get to Trieste, then 1 1/2 hour by bus to Lubljana.
Janis has suggested what might be a reasonable possibility. It's about three hours from Bolzano to Venezia Santa Lucia train station by train (with one change). The GoOpti van that I took from Ljubljana to Venice took just about three hours. You would need to give yourself about one hour (at least 30 minutes) to get from Venezia SL train station to Piazza San Marco (either walking over a big bridge, or taking the vaporetto one stop), where you would pick up the GoOpti van. So, total travel time would be in the neighborhood of 6.5-7.5 hours for this option.
Note that with GoOpti you must pay extra to have a fixed departure time, otherwise you will have a three hour departure window and will be notified of the exact time a day or two before departure. Those three hours can easily eat away any time savings.
Trains all the way.
Bolzano to Trieste.
Treiste to Ljubljana.
The bus is faster in Slovenija, but we enjoyed the relaxing scenic train ride.
The train ride from Villach to Ljubljana is not scenic. In my opinion.
The fastest would probably be: buses all the way. Bolzano-Trieste-Ljubljana.
P.S. You will love Ljubljana. We spent 6 wonderful days there last October.
MyDaytrip.com says they'll get you from Bolzano to Ljubljana in about four a half hours (options to stop at sights along the way for extra $$) for 315 euros, 2 people. We used them from Budapest to Ljubljana last spring and our driver was simply wonderful.
I would go via Austria(Lienz and Villach) all the way through the Alps, a very scenic trip and Austrian trains are nicer/cleaner than Italian trains.