I don't think Freespace would work too well as an all out guns a-blazing shoot 'em up. Maybe a stealth game? Or at least in some engine which has the capability for some degree of stealthiness - not neccesarily Metal Gear Solid levels of sneakyness, but some degree. Sneaking around vasudan ships and whatnot during the TV War would be awesome and freespacey, whereas, say, taking out all 300000 troops that landed in Deneb by your self would... not.
You know what would be cool though? Playing as an NTF commando. You'd get to fight against the GTVA, so both Terrans and Vasudans, play terrorist (Missions where you plant bombs on Vasudan planets, steal ships to supply the rebellion, capture freighters or cruisers that you get dumped onto. etc etc.) and then, when Bosch goes through the knossos, you could have a whole big closing mission where you have to fight a losing battle against Shivans boarding the Iceni, and then, err, I dunno... a grand finale?