As people have already said, Second Son takes place after the GOOD ending. How Delsin develop his powers and didn't got killed by the ray sphere? I expect some explanation, although it doesn't have to be a good one (maybe he was inside a basement at the time, and it shielded him from most of the blast). Based on the gameplay demo, conduits are far from extinct...
I also expect Cole to make an appearance, but not in as an enemy. The "ghost in the machine" theory is a good one, and I could take it. Also, have in mind that it seems to develop in a different city than the other games.