I've probably said this a dozen times, a dozen ways on different threads, but I think the ultimate killer of faction based games is the "never-ending stalemate" factor. Protagonist players don't want to lose their chars to PC death. Antagonist players don't want to lose their chars to PC death. It becomes two opposing forces circling each other and...nothing really changes unless staff railroads something.
So I guess the thought behind this idea is to find creative ways to get players to loosen their death grip on their characters, provide some hard-earned IC victories, and suspend the disbelief that the dual tommy-gun and katana wielding villain/hero survived another nuclear detonation, got away, and the player base will inevitably groan going into next time...knowing that there's only a 1% chance they'll be allowed to defeat the bad guy.