There's nothing wrong with having a great villain. There are many stories where the villain was actually more liked than the hero! For example, the Joker in the Batman movie The Dark Knight is often considered a better character than even Batman himself. As long as the villain is evil enough where the reader is still hoping for the hero to succeed, no harm done. You could make some similarities between the hero and villain but have it where the hero made different (and better) decisions towards a better way of life.