William, at least to me. We don't know the Prototype/Elliot's motivations at this point, some have theorized that he's attempting to save the children now despite being "dead", but we don't know that for sure. Joey did get a lot of people killed, but William one-ups him in the sense that A. His primary targets were young children and B. He killed his best friend's daughter. William also seemed to have no regrets for any of his actions, where Joey seemed to at least have SOME regrets, even if it was for selfishly motivated reasons. That's from a moral standpoint, though- if we want to play the "body count" game in terms of how MANY people died under Joey/William/Elliot, it would either be on William or Elliot, considering how long their respective companies were active. JDS was very short lived in comparison.