I never pass up an opportunity to visit a Medieval European city and during two warm & sunny September days I had a chance to see Prague. Quite similar to Budapest, the city is split by a river with a a big decorative castle on top of a hill on the river's west bank. Hey, if you find a good layout for a city, why change it?
The city as a whole is quite spread out but if you don't mind a bit of walking you can see all the main tourist attractions in one day. The metro and trams are very easy to use and a 24h ticket costs 110 CZK (~4,5€). Busses I didn't try in Prague but in Brno they were very good with displays inside showing of the name of the next stop, running accurately according to the schedules on bus stops. Hotels are plenty, and like restaurants, offer good value for money (a room for two in a nice 3* hotel in September +/-50€, meal with beer easily for 10€). The traditional food is pretty heavy and meant to be washed down with local beer - I recommend both! If you like shopping, I would direct you to Palladium.
Personally I enjoyed my stay in Prague. I'd say it's best for a quick & simple city break - the old town is pretty compact but lots of things to see; everything is made easy for the tourists (and hopefully you don't mind seeing plenty of them); it's clean, cute and cheap.