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which route is better: Salzburg to Prague or Vienna to Prague?

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DH and I, fit, mid-thirties, are in the early stages of planning a trip to Prague and Austria for next May. We've been reading your advice and trip reports obsessively, and definitely want to see both Salzburg and Vienna, and we're very interested in trying to make it to Prague as well. We plan to spend 3-5 days in each city, but we're trying to figure out the best routing via public transit (bus, shuttle, or train) between the cities so we can decide where to fly in/out.

So if we're flexible on the order of visiting the cities, which Austrian city is easier to connect to Prague if our priorities are 1. scenic train/bus route, 2. shorter transit time, and 3. easier connections? Also, does it change anything if we want to try to see Cesky Krumlov en route from one city to another? (is that even possible without an overnite stay? we don't like 1-night stands)

Possible routes:
1. Prague-Vienna-Salzburg (do CK as a daytrip while in Prague?)
2. Vienna-Salzburg-Prague (stop in CK for a few hours between Salzburg and Prague?)
3. I suppose we could do Salzburg-Prague-Vienna, but that seems like a lot more time spent traveling
4. Obviously we can reverse any of the above

So it seems it comes down to which is better: Salzburg to Prague, or Vienna to Prague?

Thanks so much for your help!
- M&M

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