Regarding the thoughts that WCP/SO don't feel threatening enough, it's really the same with the other WCs. As the player, we win nearly every mission after mission, yet during cutscenes and conversations, we hear that the war isn't going so badly elsewhere. Of course, there are times when no matter how well you fly, you still don't win, eg the Concordia being bashed around Enigma and Deneb sectors.
As for the Nephilim, it's clear that the force in WCP was from the Kilrah wormhole, and Casey et al shut it down. The speech about the BW finding the bugs in Valgard - "Where's Valgard? And who cares? I wanna know how the got here!" - I think was just to help enforce the idea in the player that Confed thinks the bugs were just leftovers.
Later, we find that the bug infestation in Sol is clearly from Proxima, and in the fiction, we hear about indications of more wormholes. Which leaves an interesting question: what is Confed going to do about the captured Proxima wormhole? A while back I suggested that we could use it for an invasion for the next game (understandably, some people are sick of flying defensive) but we then established that any such force would either get hammered, or have to be huge... and get hammered anyway.
Looks like they'll just take Maestro's advice and "mine it. Maybe even lob a few nukes at them"...