To be fair, evil Cole's motive by the end of infamous 2 was to heal people from the ray field plague via activating their conduit genes. If Cole were to eventually gain Kessler's time travel ability and travel into the good karma timeline for whatever reason then there's really not much he could do, the ray field plague was already cured after good Cole activated the RFI.
Sure, MAYBE he could be fighting for the freedom of all conduits through violence as the Government still classifies conduits as threats, but how the HELL would anyone stop him? We've clearly seen from Kessler's timeline that the Beast's powers are capable of ending the world, not even evil Delsin after he obtained everyone's powers from Curdun Cay could defeat something like that, and he couldn't just go up and absorb Cole's powers either because we all know what happened to John.
Cole wouldn't be a very good main antagonist because all-round, he's just too powerful for everyone.