But, with a woman commanding the ship, The Cage was the high water mark of the series for gender equality.
There was only one other time I can remember in TOS where a woman in Starfleet commanded anyone and that was in "The Alternative Factor". I suppose in "The "Man Trap" Uhura ordered the amorous crewman away.
However there were other times when the "enemy" forces were commanded by women, in Catspaw, Spock's Brain, Scalos, the Romulan Commander, Natira not many but some.
I don't think it was just TOS though, in TNG, ENT and even in VOY a vast majority of planets leaders, spaceship captain's, expedition heads, mad scientists were all men. Unless I'm not remembering VOYAGER properly. Sure women featured highly as wives, mothers, fem fatales, lead scientists etc but the leaders were mostly men.
I think they started with good intentions in "The Cage", Where No Man Has Gone Before" even "The Man Trap" and then they had "Mudd's Women".
Are the writers just giving us what we want though, is society to blame? Most television shows, movies have men as the head of the police department, hospital unit, band of intrepid explorers and we accept it. Woman can help but men still have to be the boss (most of the time).