That's another thing that Konami did right with MGO that few other developers seems willing to do. They created female characters which could use almost every customizable item in the game that the male characters could. They each had all the voice lines that the male characters used. There was a female equivalent of everything. And what makes this so impressive is that the singleplayer part of MGS4 didn't have any of these female characters, they were all created from scratch, unlike the male characters. But then again the female characters in MGO were essentially paid DLC. Look at Naughty Dog's paid DLC: early unlocking of guns, tournament tickets, taunts, etc. At the prices they charge for this stuff, fully customizable female characters would cost 10 or 15$ easy.
The problem with Naughty Dog is probably that they used male stunt people to video capture all the moves and were too cheap/lazy to also have a female stunt-person do the same moves, which is why the current female characters look so akward. You have to remember that some developers only design what they want to give you, and don't really care what players want. All developers of online games should know by now that girls play games and female characters are wanted...don't they? I've never heard of any movement to keep female characters out of games (other than the hyper-sexualized ones). So it really comes down to Naughty Dog could not or would not not create generic female characters for Uncharted.