I guess I wonder why it's an issue at all? Going back to D&D and the idea of a caller for the party the "captain role" has been a part of RPG's since inception. Watch Trek episodes, Kirk isn't a dictator he listens and uses all of his crew. Kirk can't fix the warp engines, he can't diagnose strange signals in space or analyze new life forms, heck out side of "fire phasers" statements he does not even fight with the ship nor fly it. He is the figure head in most deals or conversations (a diplomats role), but he does not do so in a vacuum. The crew can disagree with him and shape his decisions, but yes in the end he has to make the call for the benefit of the crew and ship.
A captain in an RPG of Trek is no different than what you find in business, sports, or nearly any other group human endeavor-a leader, or captain is part of the mix in life, so why is this situation any different or more troubling? Not sure, but give my Trek inspired RPG Far Trek a download and see for yourself in game play if its an issue or if it is just in the mind's eye.
HAPPY 45TH BIRTHDAY STAR TREK!