I've been away from this thread for a while, but I noticed some people early on mentioning that you wouldn't be able to run a game set in the new series since it would be hard to explain why military and civilians would team up.
I look at this much like the Starship Troopers RPG. You wouldn't have Mobile Infantry characters teaming up with non-MI characters in a campaign and the same would be true for Battlestar Galactica. Basically the players and GM would decide if they wanted to run a military centric or civilian centric campaign. There could be some crossover characters, like a civilian scientists, or perhaps other specialists, but on a whole it would either center of military or civilian personnel. The SST RPG gives you the same kind of options for campaigns. Players can play MI characters, civilians, or citizens of the Federation.
I also think that the basing a BSG RPG on the ealier series would kill it. While there might be a few people out there that dislike the new series, on a whole there are more people out there that like the new series than don't. Plus, as some suggested, an easy one-off book in the series for the classic series probably wouldn't be too much to ask anyway. But the main book should be set in the fleet immediatly following the attack and exodus from The 12 Colonies.