Well see that is the problem isn't it? The fact that this whole new found emphasis on female empowerment at the expense of the male characters has led to writing as such, and that writing is now directed at a specific set of circumstances, of which do not lend to freedom of expression or thought, because the writers now have to confine their writing in a specific type of model. In doing so, they limit the ability to create good stories, in place of stories that are politically correct, or have themes in them. It's one thing to tell a good story. it's another to tell a story set around a particular POV and political theme. I think Science fiction works best when a story or morality play is told in a way that makes a statement without making an obvious statement, or is told in allegorical terms. Modern TV series tend to be more and more on the former side, and are suffering viewership because of it, and turning their IPs who used to appeal to everyone into a show or movie, or franchise that caters to only one segment of the populace. It's not a show for everyone, it's a show for only those who agree with the political message, and that is a recipe for dwindling numbers in any venue.
It's like the same for merchandise. If the producers of the show wanted to open up to more women, and still bring along the men, I still say they should have made the choice to keep the Doctor male, but missing from the universe. Set up a 3-4 year long stint with Jenny looking for her father, and assuming his title to keep the universe in fear of the Doctor still being around to stop all the villains out there. It would have brought along the men, and still made that appeal to the girls, and some of whom were Tenant fans back in the day, may have come along to see Jenny back in the series, whether briefly to regenerate into a new female time lord body, or to remain as herself while looking for her pops. In this way, everyone has what they wanted and no one is left out, nothing has changed to accommodate another.. What I am saying is, nothing is taken away from any fan really.. only added to it, and in the end it wouldn't have been such a big deal.
I imagine a little boy playing with his doctor who action figures, and the Doctor's daughter on the hunt for her father.. In his old raggedy TARDIS.. I can see boys and girls buying Jenny's action figure for that. Because in that case, their male identification with the lead of the show is still in tact. except for a very very small portion of the population there isn't that many boys or Men no matter how much the media and TV or commercials try to portray, that identify as female or feminine. It's just a fact that the biggest population of boys and men gravitate to strong male role models and leads. This is inherent in the human psyche as it is natural to want to have a role model that you have something in common with. Sarah Jane was a great female role model. Strong, independent, and smart. really smart. yet, she gets no praise or held up as an icon of feminism because she's not the new thing on the block, and to your point..
There have always been great female roles in Doctor who. (BUT NOT THE LEAD) which is what they always say.. and yea, that is the case, but the show has lasted 50 years on the air with a short hiatus.. and here now, after all that time, we are being told it was doing it wrong.. and yet now with the opportunity to correct these perceived inequities.. The experiment seems to have failed, as the merchandise sales are way down, the viewing figures were better then Capaldi's last season but overall sucked, and there is a definite divide in the fandom, which now the media and shill access websites are even dropping the so called "vocal minority" and are themselves now admitting there is a divide.. which is funny because the same thing is true for Star Wars and STD.. How about they just write good stories, leave out the divisive PC propaganda and preaching, and get on with great science fiction and character development??
Now there's a novel idea..
I would say that fairly often the companion role (certainly as originally envisaged) is co-lead. That waxes and wanes, but certainly in the early days and the final days of the classic series (there were doctor-light episodes before there was a word for it...usually when the actor was on his hols, or ill)
I think the fan reaction to Clara should have been a sign for how this was going to go down. The modern era made the focus of the show so tight on the Doctor, that when it stepped away from that, there was a wailing and gnashing of teeth, A bunch of the fanbase did not like Clara for that *at all* (with similar grumbling about River and Amy before her, when they looked to be stealing focus.) with the result that they were snookered...only way to get a female lead was as antagonist (missy) and then gender-flip the doctor.
Which could have worked.
Except they hired a show runner who couldn’t write his way out of a wet paper bag, or hit the broad side of a semiotic barn. He really couldn’t find his semicolon with both hands...and a map.