I share a strong preference for a "being the good guys" motif. And I don't think it's farfetched for a 3rd level character to be a captain. I don't think it's far fetched for there to be a 0-level captain. Levels are game mechanics. And captain's just a title. Consider also the metaphor of a young lieutenant fresh out of academy technically in charge but wisely following the advice of the seargent who he outranks but who has been there forever. I can see pluses and minuses to having a player-captain. But having an NPC-captain who seriously outclasses the PCs seems to me to be more trouble than it's worth. Begs the question "why are the players facing the challenges when captain NPC could just wave a hand and eliminate them?"