A strong subtheme in "Perdition" is sibling rivalry. It's clear that Michael Sullivan is a better "son" to Rooney than Connor. But the old man is unable to find a balance between Connor and Michael, and so lets Connor get away with his stupidity, greed, violence, etc.--all the vices that Michael doesn't have. Sure, Michael's primary mission is vengeance for his wife and son, but he's also getting even with Rooney for his failure to favor Michael over Conner.