Changes I just discovered during the Mission: Doomsday Device:
During the first part of the mission in the Imaga system (when you have to upload the command program) ? You can no longer assign Bridge Officers. There are no stations available.
During the second part in the Imaga system (the Ground system) ? There seem to be more Klingons with targs roaming around the areas with the consoles you need to access. Be careful and be ready for additional combat.
During the final section in the Imaga system (when you fight the Doomsday Device) ? You will find your skill tray slightly screwed up by two additional skills, "Front Shield Array" and "Rear Shield Array". These provide additional power to your shields after being caught in the Doomsday Device's beam.