A lot of games out there do have these options, it doesn't mean that it wasn't cheap, that it was time consuming but it still means there was a lot of effort. To have "gender representation" in a game the game has to have both male and female characters, which for 3d games means either 2 things. Same bones, Same animations, Same options exactly or different animations, different bones, different options.
Animations are scripted recorded movements of joints & bones of a model, the vertexs or points of each face are applied to these bones & joints, this is basic modeling 101. By options I mean if another model attaches itself, like the fallout3 pipboy, the weapons, or ascetics such as a backpack, sometimes clothes. Each one will have to have a vast array of textures. This all means a big amount of time, effort, and money. For games like saints row, this is exactly where a large portion of their budget went.
Having them different means everything must be remade basically, which means everything will take time, money, & effort.
Along with that it depends on weather or not the character is silent or not, if it is, less voice acting, less programming. If it isn't well... yeah... each time a voice sound is played a programmer has to program it, and each sound has to be recorded, most of the time there is a vast array of discarded voice acting sound files that are either unusable or simply never used due to changes in development, some changes may result in more voice acting again more time, more money.
Even the most basic accounting skills should be able to see that game development isn't cheap, it is very time consuming, and gender representation with all its PC business has no place in gaming. People shouldn't play games based off feeling represented rather a surreal experience that wouldn't happen in everyday life, and well if that is your own reason why "X" game is bad is that it doesn't represent you well then you will miss out on a lot of things.
Games really shouldn't be made to target everyone, they should be available to everyone but not intended for everyone because then you really are making a game for no one.
If you are not spending money, you are spending time, if you are not spending time, or money, you are not spending effort.
Not to mention the whole issue of a story driven game, just think about it, would watchdogs be the same if all the characters genders were swapped? How about Aquaria? Bastion? Yes it would be different, it would directly effect who those games are made for, am I saying games should only be made for one target market? Heck no, I just listed games made for entirely different audiences.
Diveristy amoungst gaming as a whole good, single monotary must please everyones representation in every game is bad, it disrupts creativity, and forces each game to basically be the same.
Cost wise, game story wise, and effort wise it doesn't always make since to play the gender options route and not every game is made for both genders as they can be very different audiences, they don't have to be but they can be.