Well, market demands do need to be considered, but the problem is that most focus groups don't exactly focus on potential customers who'll have the good sense to say something along the lines of "You know, I'd like a female character who isn't traditionally pretty, who doesn't need to rely on a masculine authority and who isn't being put through the wringer to generate pathos".
Shooters are as shooters do, and the focus groups for this type of game tend to contain shooter fans. They'll focus on the gameplay first, and when asked about character potentials, their age range might drive them to focus on hot chicks. Most of us wouldn't have minded a female protagonist in GTA V, for instance, but I'm fairly certain the focus groups didn't even once question the concept of the three leads being male.
Three objectionable characters doing despicable shit? Can't be female, they just can't be. It's part of the Western social doctrine: men are jerks and saints, and women are supposed to be saints, pure and simple.
We can harp about the games industry's lack of ambition or general sense of daring, but the fact is society is generally afraid of things that rock the boat. It's silly and unfounded, but a lot of guys *might* have rejected the potential BioShock Infinite covers in their Sans Booker form.
"Dude, what's this game with the Victorian Disney chick? You turning into a ****** or something?"
Of course, nobody would react like this upon seeing the Elizabeth-only covers. The sad truth is that some guys are still really insecure, sometimes well into adulthood.