I don't know if this is the right forum for this, but is this campaign still being worked on? I would really like to see it come out. I have some ideas for it too:
It's canon that the Ancients didn't destroy every "inferior" race they encountered, but they conquered some of them. I think it should be mentioned that, some time in the past (before the start of ASW) they encountered a species with only stone age level technology, and determined that they would make good slaves, since they were physically strong and resilient and could be used for manual labor. So they came down to their planet and, using their technology and weapons, posed as gods, and enslaved them. They taught them things like agriculture and writing, and architecture. Any attempts to rebel were easily put down. During Act 3, we can maybe have a mission where they are evacuating their bases and holdings from this planet, and perhaps a mention of how the slave race asked why their gods were leaving them, and the Ancients (in panic about the Shivans arriving) let slip the fact that they were being hunted to extinction by a new enemy. The slaves, obviously confused by this, ask how gods could be killed, so the Ancients spin a tale about "The Destroyers" being the ultimate scourge of the universe that can even kill gods, and told them that they would eventually come for their people as well. This warning eventually became the Hammer of Light prophecy (as the slave race was the Vasudans).