Rather than running from one console to the next to do three boring scans, there could open up a window with some kind of circuit diagram. You need to reorganize some parts of the diagram in order to bring back energy online or something else. This could vary in way, that sometimes u only can use what u got on the diagram and sometimes u got spare parts u may pick from or there may be a time limit, after which the diagram resets and u need to try over... (not more, starting a whole mission over will be frustrating).
And that's just one of almost infinite possibilities.
And some other kinds of mission could be an attacking life form on a planet and u have to defend a outpost / village / whatever against waves of attackers.
An idea that would make some great PvP maps: One fraction needs to defend something and the other fraction storms. Whenever the attackers take over a location, the enemies spawnpoints will set back to the next point.
This kind of map could be used to bring more enemies of one fraction onto a map: 5 klingons defending, 15 feds attacking... of course the klingons got some defensive weapons on their side and got a much shorter way to the locations they need to defend.
Hell... I could write on and on... maybe u see the potential in this.