Can anyone point out the pros and cons of each. Also bus rather than train when going from Vienna to Budapest, any scenerey?

We took trains Prague to Vienna, Vienna to Budapest. Comfortable, easy travel.

You're not thinking of bus from Prague to Budapest or vice versa, are you? If so, you're barking. That'll take way too much time. The day train from Budapest to Prague takes more than 6 hours.

Why not take the hydrofoil from Vienna to Budapest if you want scenery? There are daily departures both up and down the Danube, with a stop in Bratislava on the way. You should be able to get good photos of the Bratislava castle from the river. It's about a four-hour ride.

From what I've read you don't get to enjoy the views from the hydrofoil - it's enclosed. Take the train!

I took the train between all three cities and enjoyed it. Budapest to Vienna to Prague. The Budapest to Prague journey is very long. Flew into Budapest and out of Prague.