Zeitgeist. Roddenberry tried a command character with Number One, and test audiences wouldn't have it.
That's what GR led us to believe for many years, but according to Justman and Solow, NBC rejected Majel Barrett because she lacked the talent and charisma of a lead actor. And I have no trouble believing that.
Then it seems, because Majel was his serious extramarital girlfriend, Gene had to break it to her gently. He told her the test audience story, and that the bad old executives at NBC were against a woman having authority.
In fact NBC was all for it, the executives were progressive liberals, and just wanted a better actress. Look at Barbara Stanwyk on THE BIG VALLEY. She played a lead character with huge authority. But having told Majel this whopper, Gene couldn't put another woman in the role.
I think women's parts on STAR TREK suffered thereafter to maintain the fiction that Gene told Majel.
And then the false story of heroic, feminist Gene Roddenberry vs reactionary, chauvinist NBC took on a life of its own as it got told to fans at conventions. But it was baloney and STAR TREK was anything but feminist compared to other shows of the period.