I'm not sure what the reason for the different prisons were, but I did find it kind of cool on a pure sci-fi sort of level. It may have had something to do with different prisons to house different sorts of powers (the Big House for brute force criminals, the Cube out in the middle of nowhere for radioactive criminals?). Or it may have to do with the hidden "purpose" of each house. I don't know enough about the Marvel Rogues galleries to know for sure if there's any common pattern between, though.