Well MichaelM also said Unless I'm forgetting something about the Good ending, I think that hints pretty strongly at Second Son making the Evil ending "canon."
Keep in mind that over the course of inFamous 2, the Beast is decimating the East Coast and stated that his method of destruction was his Ray Sphere Blast, which undoubtedly created more Conduits. This could be focusing on the story of some of those people, or the aftermath of the Beast's destruction. Of course, there's always the theory that John's powers let out a large amount of "Conduit radiation" into the air and possibly affected many people over the years, and if you count weather trajectory spreading the radiation all over the US and possibly the world, there's a chance that Delsin caught the strain when he was 17 and his powers remained dormant until they exposed themselves in a moment of extreme stress, in this case the bus crash and in Cole's case, the RS explosion.
This could work in the Good ending too.