What about a system for intercepting and boarding another ship? You could have a pirating scenario where you aim to disable ships, board them, take their stuff and then sell the booty for cash to upgrade the ship. Yar!
I'd definitely like to see more complexity at each station, as well as tasks that require co-operation between crew-members (e.g. the tergetting system suggested above requiring both science and weapons consoles). I like the idea of each console being its own 'mini-game', although I'd be careful not to make things too abstract (The hacking in Bioshock 1 and 2 comes to mind as a bad direction to go).
I haven't played with a real crew yet, but running several consoles on my desktop was actually pretty fun, if a little impractical :)