I would love to see a group of missions in the mirror univrse. Something like a base set up at a stable gateway (think DS9) that is used to explore and make allies with the Klingons and Romulans of that Universe to help overthrow the Terran Empire. Lots of Dipolmacy, some combat until the final arc where you fight to help the rebellians.
An interesting concept for an episode might be that one episode of Enterprise . You do a mission entirely from the POV of your Mirror Universe counterpart and have to be sneaky and evil to complete the mission. The real you doesn't appear at all.
Also, I was very disappointed that I didn't get to fight a Mirror Universe version of my ship in the mirror universe missions that are already in the game. Maybe this could be done with branching dialogue trees or something. Someone asks you what class and name your ship is and it spawns a "I.S.S. Yourname" of the same class.