Were there any back stories in mind for the villains of hero factory?For example Meltdown, what's his back story?
Unless a back story showed up in one of the books, no. The story bibles I saw generally did not go into back stories, and I only came up with them if I needed them for a book.
The best resource I've found for these things is Makuro's Secret Guide Book. Even so, they're quite bare bones.