3 hours in Vienna or Beatislava

That's so little time (some of which would be spent storing and retrieving luggage) tat I would opt to use the extra time at either your starting or your ending point unless you already have a lot of days allotted to both Prague and Budapest. How many nights are you spending in Prague and Budapest?

oh ya I know you're right but I have days allocated already 2.5 days in Prague and 3 days in Budapest and my travel time from Prague to Budapest is 7 hours which I don't want to do in one straight journey. Hence wanted to stop in Vienna or Bratislava for a few hours and then head further to Budapest.

Between stowing your luggage and getting your bearings, you'll only really have time for lunch. That said, it's just 2 U-Bahn stops from the Hauptbahnhof in Vienna to the inner city, and that's where I'd go for lunch. I haven't been to Brataslava, but everyone I know who has says it's not particularly exciting, and Vienna is exciting. The downside is you may regret not giving Vienna a couple days instead of a couple hours.

When the weather is fine, you can enjoy the Belvedere gardens which are only a 10-min walk from the central station (Hauptbahnhof).

Personally I would fly between the two and eliminate the problem all together. Czech Air nonstop for about $100.

Otherwise, Vienna makes good sense. Just walk out of the station and you are in the middle of it.

For me that wouldn't be enough time in either city, but if you are not comfortable sitting for seven hours on a train and don't want to fly, I guess a stop is in order.

If you could stretch the stop to 4 hours, I figure you would have about 3 hours to look around (assuming 15 min to store luggage and 15 minutes to get to the center, and then the same in reverse to get back. That might be a bit optimistic.) I think you can do it if you have a plan when you hit the ground. I don’t have any specific suggestions.

Vienna for sure. It is an incredibly beautiful city. After spending time in Prague and Vienna, I felt that Bratislava was very underwhelming.

While I also think you should fly, I know both cities. I’d pick Vienna. Take the U1 to Stephansplatz, walk down the Graben, take a left on Kohlmarkt, walk through the Hofburg to the Ring, turn left on the Ring and have lunch at the Palmenhaus at the back of the Burggarten. After lunch, walk past the Opera House and get on the U1 at Karlsplatz where Hauptbahnhof is two stops away.

Vienna is a great city. Think Chicago or San Francisco. It's a world city.

Bratislava is a minor capital. Think Nashville or San Antonio. Certainly there are things to do there, but it's not a world city.

I'd pick Vienna, but as others have said, you will probably ask yourself why you have to leave.