I was just thinking of another concept for a mod: a (possibly) multiplayer scenario in which there are a few different plot lines and you must choose a side to fight on, much like in Starcraft or Escape Velocity.
It would also be cool to have scenarios that have bosses with beefed up life/hit-points, especially if they shot out bad guys to attack you while you fought them. Or maybe one you couldn't kill with your weapons but instead had to activate various switches to crush it with a platform. Once this is done, you get a new weapon or power-up that teleports in.
I think powering the player up with new weapons and items as you go along is a cool idea.
Would these things be hard to do?