Wasn't there a game once based on the X-Files?
Take the X-Files feel, and apply it to the game. I've toyed with the idea of having a single villainous faction (which sets the tone of the game, and you can cycle these at a long running enterprise of a MUSH), and having two heroic factions with cultural differences. This would not only unify villains, so you'd have a single backbone for conflict, and form them into a unified clique that would be forced to roleplay (tis the nature of the villainous beast), but also split your heroes to prevent the size of the traditionally popular opposition from overwhelming the villains.
Add in something in the cultural difference between the heroes that creates an opposition that evokes interest in both social and intrigue roleplay, and you've got yourself a winner.
Following the government conspiracy theme: A paranormal syndicate as the villain, a clandestine investigation agency with tight government control as one hero faction, and an underground resistance made up of individuals burned by said villains as the other faction. The paranormal syndicate would create the backdrop, the investigation agency would be attempting to check the resistance, and the resistance would want more alarmist measures that the government agents would have to control.
You'd have the level of the syndicate trying to influence both the government, and hunt the resistance, while the agents would be fighting the syndicate and trying to protect/reign in the resistance (for their own good), with the resistance trying to evoke moral empathy for their cause from the government agents and be participating in dramatic actions against the syndicate.