Both comics and games suffered from marketing and advertising types coming in and saying “Hey, there’s fighting and killing in this thing, we should market it exclusively to boys.” That’s why Wonder Woman started out in the Justice League as their secretary (seriously, an icon of female empowerment as the secretary of macho men), and all the ads for games in the late 80s and early 90s stressed the idea of them as a boys’ club kind of interest.
I think what it ultimately comes down to is that whenever a medium is in its early days, it’s pretty open to any comers. But once it starts making big bucks and developing into a cultural phenomenon, you get people coming into it that insist on injecting social biases against women in the misguided idea that it’s where women “belong.” We’re getting a lot of that idiocy lately toward women in the indie scene for saying a single criticism against the “typical game” as some see them.
Before I end off, I just want to say that I place a divide between fanfiction and official work. In fanfiction, I’d be cool with stories where Wonder Woman acts as the Justice League’s secretary, and I might even do some bizarre writing of that idea. It’s just fanfiction, after all. It’s different when it’s the official product a company puts out, meant to be the defining representation of that character.