First, as far as the AI for right now is concerned, "move -> turn -> shoot" will at least give people something to shoot at - get their target practice with. When we add networking, it will likely be even better. I think this is a good starting point until we get something more sophisticated.
Second, as far as the AI in crewmates is concerned, I agree with the idea of having an NPC be the engineer / etc. Some people might want to do that kind of job on a ship, but most likely won't - they'll want to be piloting or whatever. NPCs could do those jobs (similar to how we as a society are planning on having robots do those kinds of jobs in the future). In the example given, the AI should automatically realize that the engines are damaged and begin repairing them immediately, unless given prior (or countermanding) orders not to. You never know, the captain may need those resources for the final laser shot to blast the enemy cruiser into the unknown...
We also need to plan for the flightsim, RTS, and FPS aspects, and the AI associated with them. I already have some ideas for the RTS / FPS interaction, so I'll post those in a separate thread later. As far as the AI goes for the current flightsim aspect, I'd say mcrobotics is on the right track.
~Brian