You know, a Wing Commander 6 (chronologically speaking; or 7 or whatever you want to call it) wouldn't necessarily have to follow a "Nephilim trilogy". While I'm sure us fans are dying to know what happens, here's a scenario that's perfectly realistic:
1) The Nephilim, after Secret Ops, never show up again. Just as it's a completed mystery as why they showed up in the first place, it's an equally complete mystery as to where they've gone off to. Perhaps they're retooling their invasion plans for a future date, or it takes a long time to regenerate the wormholes. Assuming the Nephilim had contact with, say, the Kilrathi in the past, thousands of years between invasions isn't unreasonable. By then, of course, all of the current batch of characters will be dead.
2) Of course, this still leaves the fate of the Prophecy cast up in the air. Two possibilities of dealing with this. Either they could simply be shuffled around off scene, or to cameo parts at the most (as happens from game to game; new characters pop up, old characters simply disappear for misc. reasons), or they could keep the current cast but make a non-Nephilim-oriented story, or they could actually do a Nephilim story based on #1, thrown a thousand years into the future, making a clean break with current history.
So you can see, a continuation of the story doesn't necessarily imply Prophecy with better graphics/gameplay/multiplayer. LOAF has a pretty good point, though, about how a prequel game, or a radical departure on the gameplay formula (like an online component, "massive" or otherwise, or a genre bender) would probably have a better chance of making it through the strategic decisionmakers at corporate EA.
Something to consider, though. While I'm just speculating wildly here, it could be that there's hardly anyone left at EA who wants to pitch a WC game idea. If I recall correctly, a lot of the people who were really involved with WC were laid off, and a number of them probably want to move on to something fashionable and new and perhaps more commercially successful, so they can keep their jobs, and just for the sake of trying something new. Over time, franchises can be forgotten, even if they were once popular serial series, and be relegated to the dustbin of gaming history. It could well be that we won't see another WC game until someone 10 years from now decides they want to do a "remake" of classic 1990s gaming action, except with
modern gaming technology like UltraMegaPrecision TriDimensional HyperTexel QuadScopic Light Acceleration XIV (TM) (as featured on the latest ATidia RadeForce 955900 XLPTRQ). Of course, someone with some actual knowledge of what goes on at EA today could perhaps provide speculation somewhat more grounded in facts.