Skills would pertain toward crew members, and they would describe exactly what a crew member is capable of.

Major skills:

• Command (help manage staff)
• Engineering (help manage equipment)
• Navigation (points the ship in a direction)
• Tactical (fires weapons in a direction)
• Communications (reach out and touch someone)

• Command:
• Executive (micro management for the whole crew)
• Engineering (good at overseeing/aiding/managing engineers)
• Navigation (knows maneuvers, good at giving orders to pilots and such)
• Tactical (good at managing gun crews)
Commanders would also likely have experience in the field which they specialize. The Chief Engineer would obviously be able to help out in repairs, just as a Navigation Chief would be able to take the helm, or a Tactical Chief the trigger.
• Engineering:
• Hyperdrive tech. ("She'll have be offline two hours for repairs after that stunt")
• Weapons tech. ("Coil gun fixed! Launch away!")
• Shield tech. ("One more hit and she's gone!")
• Scanning tech. ("Scanners back online. We're no longer flying blind!")
• Ships systems ("Yup... that busted sewer pipe means MREs for breakfast tomorrow.")
• Comm. tech. ("They blew out our antennae relay!")
• Thruster tech. ("Peanut butter? How'd that get in the thruster?")
• Computer specialist ("Why do Macrosoft products always have bugs?")
Engineers might have some practical experience at operating the equipment they repair, especially the specialists...
• Navigation:
• Scanner readings ("Set course vector 5-5-4 to intercept.")
• Piloting ("Setting course...")
• Combat manuevering ("Evasive manuever kappa-kappa-pi!")
Conversely, Navigators might have some limited experience in repairing their equipment.
• Tactical:
• Weapons management ("One more shot before it overheats!")
• Weapons Control ("I could shoot the fleas off a dog.")
Weapons operators might too have the limited ability to fix some problems with their weapons.
• Communications:
• Diplomacy ("We come in peace and/or furor.")
• Negotiations ("Maybe we give you two credits for that?")
Communications specialists too would be able to make limited repairs of their equipment.

Crew members might display specialist behavior or generalist. Specialists would be desirable for larger ships, while a small ship would need generalists to keep it going. Generalists would never display the level of sophistication as specialists, but they would be far more flexible.

For ships with smaller crews (say 2-4), you'd have to adjust your priorities yourself. Obviously an engineer is more useful than a communications man, and a weapons operator more than commander on a small ship. And there'd still be one seater ships where you have the pleasure of taking care of yourself and being the ultimate generalist.

We could also have general skills, if we wished, which would take certain skills out of different categories just to indicate human flexibility, but they'd have to pale in comparison to specialists. Imagine a communications guy trying to fire a coil gun... obviously not a good idea (or an engineer trying to communicate ;-) ).