Wait a minute... replace how? Sorry to break it to you, guys, but FreeSpace has been defunct for almost a decade now. The new batch of gamers don't even know what it is (granted, they don't know what anything is- kids honestly do seem to get dumber and dumber every generation). There's no "replacing" to be done except that which has been taken care of by pretty much all the fighter sims to have come since FreeSpace. End of story.
If you mean as far as gaming itself goes, they share only some very basic aspects. FreeLancer is much closer to Elite and Escape Velocity than it is to FreeSpace- if anything, I-War 2 replaced FS there, even though EoC was a marketing bomb. It had far superior graphics (no ****), better plotline than FS2 (both plots sucked ass, frankly, but EoC's had pirates), and what is generally considered a better flight model- and I'd agree if I wasn't so wierded out that I was a god at combat in the original and hated it in the sequel. It was highly linear, though you could go off and steal stuff to your heart's content, and had all the weapons and toys you could find in FS and more.
Of course, on the other hand, one of them I can't abide whereas the other... well, I'm here, aren't I?