Hello there (please note that whatever is written here maybe complete garbage or it may have been posted before.)
In had not touched my inFamous games for quite a long time but when the Second Son was announced, I decided to replay both of them (or at least the main missions).
As I finished both however I noticed something. There is a major difference between the Beast from Kessler's timeline and the Beast (John White) that we face in the second game. Allow me to explain. The goal of the Beast in Kessler timelines seems to completely destroy the world (and beyond as evidenced by the shattered moon in the background), however John's goal is to force mankind's evolution so that they may survive the deadly plague.
Then something else came to mind. Kessler was the leader of the First Sons, an organization focused on advancing humanity. Furthermore it would seem that Kessler was aware of John's nature through one dead drop in inFamous 2. So what if the John was but a tool of the First Sons? I mean, Kessler did want you to activate the ray sphere a second time (I think) and generally be a ruthless, cold-hearted individual. After all this, the idea of Kessler plotting you to team up with John to advance humanity does not seem so farfetched to me. What's more is that with all those blasts that were needed to activate the entire conduit population, Cole's strength would be amped up to. Perhaps Kessler did not only plan to prepare Cole for the arrival of the Beast but also the whole world. After all a world full of conduits would be much harder to destroy than a world of humans, right?