Geographically, Budapest would make more sense than Croatia if you're coming from Vienna. Budapest is an awesome city with a good mix of sights and nightlife, and it really feels less touristy than a lot of the other popular destinations in that part of the world. I was there for 3 nights and that seemed about right, but you could do it in 2 if you need to. The Budapest to Prague train will take you right through Bratislava, but I'd skip it.
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