It's a continuing peeve of mine that this game doesn't have multiplayer capabilities with regard to individual ships. I know we can't realize the style of combat seen in the shows with respect to the various systems under this engine. In fact, that might well make for boring combat, and be generally frustrating for all.
In light of that, I propose a set of 3 basic minigames for the ship interior. These minigames to correspond with the 3 career tracks. One to be placed at the tactical station on the bridge, one to be placed in sickbay, and one to be placed in main engineering. The operation of these minigames might be as simple as using an arrow key to match a corresponding icon as it scrolls past a marker line or somesuch. Say, 20 icons to match, and the score of accurate hits is multiplied by 0.5. This number is then applied as a non-stacking combat buff to the hosting captain's ship as a 0.5 - 10.0% bonus for 5, perhaps 10 seconds to accuracy for tactical, crew heal for science, or recharge rate for engineering. Naturally, the system should just skip applying the buff if the ship is not in combat.
I don't pretend it's a supreme idea, and it's probably not something players would want to do constantly. However I could really enjoy having this option for Fleet Actions, STFs, PVP sessions, and other things I do with my fleet as a group. Just throwing it out there, this has probably already been offered up. A mere attempt to contribute constructively.