"The idea of having a navigator, a gunner, an engineer, a pilot, soldiers. mechanics, fighter pilots all in the same ship seemed like a flight of fantasy."

I would be imaging rather this:

Group of 3 players has just left planet Alayon in case of transferring medicine to another system. Just after they enter the open space, two pirate clan fighters enter the system. To reach the hyper jump area (out of planetary gravitation) they need to wait for at least 2,5 min. Navigator chats over text chat: "Pirates!!! Come quickly" Other 2 players, who have been playing some minigame runs quickly to weapons, other back, other up. Navigator screams: "Fighter ahead!", Upper gun man responses: "I see it!" And fires.. Intensive battle starts. Navigator tries to dodge enemys fire and upper gunman (who see only up and front) and back gunman (who see only to the back and down) tries to disable enemy attack. Pirate missile hits engine and navigator screams: "OMG, the hyperspace engine has been broken.. Leeroy! Go and fix it!!" and back gunman runs quickly stairs down to the engine room and another missile hits. Player can actually feel this shaking in his foots while he tries to get in to the engine room. He starts to fix it and some wires has been melted and he must remember what did go where when he connects them. Upper gunman manages to destroy one of the ships but lose the other. The pirate player understand that there are no firing from the back of ship, so there is a safe place to be. Upper gunman asks navigator "Where the he** is that ship?!?" Navigator screams. "It's behind us" While back gunman is fixing the engine, upper gunman must run to the back of ship. Then he waits until back pirate ship is locked to missile and FIRES! It misses, but navigator has reached the point where one can enter hyperspace and engine is already working. Whoooozzh.. They flies to the safety.

Other pirate ship didn't have tracking computer so it can't track the transporter and has to satisfy to collect another pirate player from floating around empty space and remaining of the other ship (after heavy repairment most of the parts can be used again