In theory, that would be a great idea. A problem with ongoing comics is the villain will always escape prison no matter how well or where it is built. However, if you were doing a story where that was not a factor then yes doing something like you suggest would be a great idea. Either that or give high-powered villains to the Guardians of the Universe to imprion. Either way, the prisons would be more capable of holding them than Earth-level tech and if the villain did escape there would not be a city near by to trash.