Super Soaker Collector / Administrator
If you don't want it Lucas-ified then prequels are not the way to go. I already know what happens with the Kilrathi war, and I don't want to play any more games set then. I want to see what happens next. Frankly, I would have liked to see them continue the story with the bugs and make a proper trilogy, although the opportunity for that is basically passed now.
I think prequels could be very well done. The Kilrathi War is the most popular WC setting, and we haven't been exposed to the vast majority of it. This goes back to the definition of an epic setting though. Do we need to have any influence on the war at large? Does it matter what war we're in? A Kilrathi conflict is practically a given, but the most powerful stories can be small scale.
They could make an amazing game that's all about escorting a medical transport somewhere - your family is on the ship, you're flying off a destroyer with just a few fighters aboard, suddenly you all find themselves trapped behind enemy lines and need to make it to safety, so you raid a small Kilrathi outpost for supplies, stumble upon a high tech weapons cache, accidentally find yourself rescuing a Confed corvette that then joins your flotilla, etc, etc, etc. Individual games don't have to be about a galaxy-spanning four-decade war... that's just the backdrop.