I've got the plot for a great prequel set between the destruction of the Tiger's Claw and WC2!
See, the Kilrathi develop these new 'Phase Shields', and a brand new Dreadnought (like the one that got Goddard) is the first ship outfitted with them. Since torpedoes haven't been invented yet, and all the cap ships are armed with laser turrets, no one can touch the thing, and Confed is forced to mount a last ditch effort to halt it!
I SWEAR the resemblence between this scenario and Freespace is ENTIRELY coincidental...
Besides, I can't remember who invented Phase Shields, and knowing my luck after suggesting something like this, its Confed.
Seriously, though, if a game were a prequel as opposed to a proper sequel, I think I might like to see something set during WC1 or WC2 (or between). With any luck, it would also have a multi-player component (finally), with a full-blown mission editor similar to the one in Freespace (which allows a creative player to do just about anything), and the ships from at least a couple of different eras.