At the end of Watchmen Doctor Manhattan explains that he may decide to go and create life before leaving Earth indefinitely. Throughout the history of the DC Universe and namely that of COIE, Multiversity, an episode of JLU, and other media a Cosmic hand has been shown manipulating and creating the cosmos and the Universe in DC Comics lore. That hand has always been a pale color but most recently it has been shown to be blue. In Rebirth we see the hand reach down and manipulate things. We see this in many different stories as well.
I posit that Doctor Manhattan is literally that Cosmic Being that has created the DC Universe as his form of life and his power has a side-effect which gives off the DC Universes superpowers in metahuman genes.
I believe that Superboy Prime learns of Doctor Manhattan and Watchmen and after having his own time in places like the Source Wall, living in prison on OA, and also having an Omnibus of knowledge that is the DC catalog he has broken the Universe to finally create the perfect world that he, Kal-L, and Alexander Luthor sought in Infinite Crisis. He is creating things the way that some fans see the Universe logically and he may even be in way over his head as the continuity is utterly broken and he may not be able to keep it straight. I believe that he is Mr. Oz and he is forming an army to take on Dr. Manhattan in order to keep his universe the way he has made and that of Doctor Manhattan is trying to fix the mess he has made.
I believe that Doctor Manhattan is actually the good guy in all of this and it will come to pass that the Watchmen aren't actually characters in the DCU at all but that of another plane of existence. They are however obviously bleeding over into our world. Will we actually see Veidt, Owl, Silk, and Rorschach? I think not. I did have a theory that Rorschach may actually be the new 52's Question as he is cursed and doesn't remember who he is which would be Superboy Prime or even Manhattans way of not letting anyone spill the beans about the Watchmen characters. However, that theory was shot down by Scott Snyder last week at Emerald City Comic Con. So Booo---Urns on that.
However, I would love to hear thoughts on this. I think evidence is mounting that all of this may be the case.