Im a bit short of time so I will have to keep this short.
I studied for 2 years in Prague (second faculty) and now study in a city called Brno.
The university in Brno costs $6900 per year which is a lot cheaper then Prague. The quality of the university and teaching is a lot higher in Brno compared to Prague. The city itself is not the most interesting of places in relation to Prague however both Prague and Vienna are both a short drive.
http://www.muni.cz/
If you do decided to go to the Czech republic you have to understand that the workload is a lot higher then other places in the first 2 years.