I think one thing Battuta touched on that I have to disagree with is the whole thing about innovation. Innovation has been prized (perhaps too much) by Western artistic thought in the last 200 years or so, but that's only a rather small part of what makes an artistic work good. A well-executed iteration will beat a mediocre innovation. Consider the "Old Masters" of European painting--these artists, from around 1350 to 1700, produced some of the most beautiful and well-regarded artworks in human history. They also were openly and unapologetically derivative--hundreds of pietas, madonnas, and other stereotyped forms, in roughly the same styles, year after year with innovation happening very slowly over the course of generations. There were fewer original ideas in those 350 years than from 1850 to 1900 alone, and nobody cared.
That said, creating a successful FreeSpace series would require you to end up with a rather different thing than what you started with, due to the nature of the two media (and a serialized TV show is itself an altogether different beast from film--blow up a TV episode to feature length and the result is an abomination like Star Trek: Generations). I would say the Terran-Vasudan war would be an easier setting to work with than the two Shivan wars--the Shivans are more like a force of nature than an enemy military, which severely limits their storytelling potential as antagonists. Vasudans, on the other hand, are people humans can understand, and a lot of "meanwhile on the PVD Whatever" stories and meaningful interactions with humans are possible.
The Talania system is a huge blank in the FreeSpace continuity. We know that it existed, there was a decisive battle there, and the system is no longer accessible. That would be my obvious pick for a setting, due to the massive unexplored potential (also, because of the stalemate nature and extreme length of the war, it is likely that decisive engagements were very rare so a broad overview of the whole war would likely be rather dull).