I'd like to return to the Nephilim war in a way that requires no knowledge of Prophecy/SO. There's a few options, a Shenmue for XBox style movie of Prophecy, a remake of the game etc, but I think the franchise needs to move forward.
My suggestion, off the top of my head, would be to jump forward time, to a character that lost his family during the events of Prophecy/SO (I know I know, another orphan), this would give the writers a good window into those events for people new to the series but allow for a 21t century reboot.
The war having taken its toll, present the kind of bleak outlook we saw in some of the earlier games, put the confederation at the brink of defeat, really convey the scale of the conflict somehow as well. Normally I'm not a fan of dark scenarios as there's a tendancy to populate them with buzz cut marines to save the day, but Wing Commander always did character very well, each person hanging on to their sanity (or not) in his or her own way.
Story telling is crucial to me, I know this is outside the confines of the topic but I would like to be able to explore the carrier personally, talk to various characters if and when I choose to. I've long had this image in my head of the scramble alarm going off from a surprise attack, and being in control as you run to the fighter bay.
I do agree however that the Kilrathi are the more interesting enemy, but we should remember how far they were developed, and how comparatively little attention the Nephilim got. If anything however the lack of exploration just leaves the door wide open to new ideas. Besides there would be plenty of room to explore the Kilrtathi as a race, even if they were just allies.