It might have to do with these two things:
1. Most gaming controls are a bit too complex for beginners in general.
2. Mainstream games require a lot of time and attention investment that a lot of women I know don't have.
As a female that's been gaming since I was a toddler, I've only found controls getting easier as I get older and I'm used to organizing time for games. Other girls my age that don't, typically spend more time doing other things and don't know where to put games into their daily timetable.
"I can't, I'm going shopping for makeup with my aunt and tomorrow I've going to meet my friends at the cafe in town."
"It's been so long since I last played "Call of the Warfighter's" tutorial level, I've forgotten how to play it again!
I don't think it's for me."
Using my mum as a basis, since she has tried playing new games a lot of times and enjoys them when she has a chance, a fixed camera angle is usually a plus. 3D orientations confuse her easily. She can't get the hang of controlling the camera and the character at the same time.
My dad sometimes has the same problem, but he will still figure it out after a while (He REALLY likes Halo). She can't.
Out of the games she likes, most of them are 2D because there's no extra plane to worry about. Angry birds on Android, Peggle for Xbox 360, Bejeweled on a PC, Bubble Bobble for PS1, Casper for PS1, Pitfall for Gameboy, The Fish-Catching minigame in Jak and Daxter for PS2... She always enjoys them even if she fails because at least she can figure out why she failed and how she can improve on what she did. Even after she's put the game down. She can go back to it and still remember how to play because she doesn't have to worry about the 3D aspect. Even if the games themselves were rendered in 3D, as long as they played in 2D there was no problem.
And there is evidence to back this up. Women during scientific studies have, on average, had greater difficulty navigating 3D spaces than men do.
It's overwhelming and a large barrier to overcome in an industry focussing more on graphics and less on gameplay.
If every room looks too much the same, if there's no in-game map or compass, if there's no identifiable landmarks to remember so that you know you're not going in the wrong direction but a tonne of identical hi-def trees, it would confuse most folks anyway. But I'd imagine newcomer girl and women gamers would have a harder time with it.
And that's if they've got the time to play for long enough to learn the environments in between looking after kids/pets, going to work, doing housework, buying groceries, etc.
Even though a lot of these tasks are shared nowadays, there's still a lot of women doing most of the main jobs around the house as well as childcare and work. Good luck trying to follow a story with all that going on! Add going places with friends and family to that list and suddenly women not playing COD as religiously makes a lot more sense.
Most games that women like tend to be pick up and play. Something you can learn in a minute, put down in two and then pick up again when you're done with what you needed to do. It's another reason why my mum likes them. She is mostly bedbound thanks to her spine but still cooks the dinner most days, washes dishes, cleans up and organises appointments as well as manage her pain medication and other things.
She couldn't play FFIX even if she tried with her many distractions. If she's reading the screen and suddenly it's 6pm and time to put the chilli con carne in the slow cooker, she won't be able to just stop playing. She'd have to find the next save point. But before she's got to do that she has to either skip what's being said and never read it again or hold out for another hour until it's all finished.
It just makes sense that there aren't as many women playing games. It's nothing to do with marketing. There aren't enough female game testers and developers to say where they or their friends might find it more difficult to keep playing. When those problems are addressed, then games will be more accessable to female gamers.
