IMHO i think this could be quite an experience and somewhat of a burden of the narrator - if you are going to crew more than one ship with NPC'S you need at least all departmendheads fleshed out.
Getting these together without to many stereotypes is probably the most complicated task.
Alternatively you could distribute the NPC's among the Players, so they have there hands full as well, and have something to interact with the peculiar Captain of a given ship. If you have Five Players, a player might be the CO of vessel A, the XO on vessel B (otherwise an NPC) , the Chief Engineer on vessel C (also an NPC), the Flight Control officer on Vessel D and finally the Tactical Officer on Vessel E.
If all are Focused and are prepared to jump to the scenes this could be quite an experience. On the other hand -as a worse case scenario- it could turn out to be an nightmare of epic proportions. Anyway there is a hell of administrative work ahead.
"Space may be the Final Frontier, but it's made in a Hollywood basement"
Red Hot Chili Peppers "Californication"
"per aspera ad astra"
Seneca