Sounds like a great project for the community – I hope it reinvigorates some peoples' enthusiasm

Regarding the gaming mechanics, I'll leave that to older heads, but you might make a note that these games would be perfect for helping playtest and give something back to the community.
Background-wise, and as something a bit different, have you considered setting it during the
Nova Terra Interregnum?
This was a period where the Ur-Council of Nova Terra rejected the authority of the High Lords and declared the Segmentum Pacificus a separate domain from the remainder of the Imperium.
It would provide a great way to pitch Imperial forces against one another (judging from the sign-up thread, Imperials are the largest faction), as well as explaining the variety of other species and factions involved – resurgent xenos, heretics and mercenaries taking advantage of the conflict. It also gives a great sense of scale – you can have whole systems falling or being recaptured, and regardless of the result (e.g. does the Segmentum Pacificus grow or shrink), it makes no huge difference to the current state of 40k (since the Ur-Council was eventually overthrown and the Segmentum reabsorbed).