I always read Kirk, Spock, Scotty and Bones as being senior to the rest of the bridge crew (in age and rank), but the movie crew was *determined* to shoehorn them all together.
It's been suggested elsewhere that when Spock was being de-briefed by Starfleet, he revealled the importance of Kirk captaining the Enterprise to the safety and security of the Federation. A plausible fix, and would have taken five minutes of screen time. But, I think that's this movie. They did "the cool thing" not the plausible thing (Scotty transporting into the plumbing, bridge crew running all over the place, gattling phasers, monsters eating monsters chasing Kirk, on and on...)