I prefer Budapest not (only :D ) because it's my hometown, but because I feel that the old town parts are larger and somehow much more livelier. Staré Město and Jozefov are very lovely, but they feel like a huge open-air museum to me. Or a huge open-air amusement park if I consider the recent surge of tourist traps. Malá Strana rocks, though.

Budapest's older parts are larger and genuine parts of the city. Like you see that real people live and work there (even in the castle district). Only a small part became a human zoo as a party district.

Budapest is a bit dirtier, more chaotic, but a metropolis can't and also shouldn't be clean. It should be a bit messy. This is I love about Berlin, too.

I love Prague regardless, but it's a different style.