This isn't a post to tell you not to take a side trip to Bratislava, but rather to prepare yourself for what happened to us a couple of weeks ago.
We decided to take an afternoon to explore Bratislava so went to Wien Hbf to purchase our Bratislover tickets. The ticket agent said the main train station in Slovakia was closed due to construction but we would arrive at another train station and a bus would take us the rest of the way. So I thought, no problem and envisioned a nice bus waiting for us when we arrived.
The reality was quite different, however. We arrived at Petržalka Station to mass chaos. There were a lot of tourists. Slovakian ticket agents seemed overwhelmed, unfriendly and lacked English skills. We were on our own and tourists started banding together to help each other out. My wife and I teamed up with a mother-daughter couple from Spain as my wife speaks Spanish fluently. We met some locals who helped us and it worked out. We worked together to get to the tourist area then disbanded.
Petržalka Station is actually not so far from the old city center. The problem was more of communications one and less of a logistical one. Dummy me forgot to preload the Bratislava map in my Google Maps iPhone app. My intent in sharing is not to discourage you from going but rather to spare you the confusion as it's not hard once you know where to go
So if this happens to you and end up at this horrible little railway depot, do not panic. The station is very close to where you need to be. If you end up inside you will want go back out toward the train you left and walk through an underground walkway in an easterly direction. The street you will come out on will actually go directly to the old city center so cross the street and take a bus north. You may want to ask a local which one as there seemed to be several that went in that direction. I forgot the name of the stop you need but it was the first or second one after crossing the river.
I hope this helps someone. If I were to go back I would know where to go right away and it's not too hard.