Which side of the train do you recommend
As both routes are not very scenic it does not matter where you sit in the train.
Actually scenery between Chocen and Brno on the line Prague - Vienna is not bad. Wooded valleys, rivers, toward Brno valleys become deeper, many tunnels. Because scenery alternates (at one moment is better at right at the other on the left hand side). Scenery between Vienna and Budapest is not particularly memorable.