This is a very prevalent issue. Unfortunately, it probably won't change until there are more women in the industry. Gaming is male dominated, as are most industries. The New York Times article you used about The Last of Us made some good points. I felt like Naughty Dog could have gone much farther with Ellie than they did, but how can a 30 something-year-old male programmer or writer relate to a 15 year-old girl who lives in a world under martial law with a form of cordyceps that affects humans?
It's easier for a man to relate to a man. I have never met a man who can sit down with a woman and talk about how periods are a curse or how breast-feeding takes a lot out of them. If the gaming industry doesn't have many women, then how are they supposed to make games that can relate to women?
Many colleges are giving scholarships to women for computer science degrees, because in that field, we are a minority. I was a Computer Science(CS) major for a while. There were only girls in my class including me. Out of 70 class members, only four were female. I switched majors because I couldn't program at all. I didn't understand my assignments even when they were explained thoroughly, but some of those other girls would be done with their assignments before the next day.
This can go back to what we are always told: boys are better at math and science, and girls are better at grammar and literature. When society beats it into our heads that no girl can succeed in a math or science related career or that nerds permeate a certain career, we don't want to go into that career. You know the number one reason I got when I asked other girls outside of CS, who could have done it, didn't? Because the guys were creepy and they didn't think they could do it because their math scores weren't high enough(that came from a girl who had top scores in a college level Calculus class). Yeah, some of the guys were creepy, but all in all, most of them were alright. I couldn't talk to them about some things like having guys stare at my chest(since they did it too) or running out of pads and trying to buy some discretely.
One solution to sexism in gaming is to get some more girls in there. Games like Skyrim or possibly Fable( I say Fable because the clothes can go either way on a male or female character, plus you can make the males were makeup and corsets) make the male/female decision almost obsolete. In Skyrim, it doesn't matter if you are a female talking lizard. You are still the Dovakin. In Fable, you could play as a woman, wear men's clothes, and be fat. You are still the Hero of Albion. If more women join the ranks of EA, Bungie, Activision, Ubisoft, Naughty Dog, Valve, etc., there might be more games with women as leads.
But The Last of Us isn't an RPG. You are stuck with Joel as a lead. We can't change the past. We can only change the future.