Long time lurker. I am female and an artist. So, here's my two-cents.
Art is something generally left entirely to public interpretation. For those who want to argue this basic fact, look to advertising industries. Ads use art all of the time to generate an emotion or use cultural associations to create an idea. Children can explain this logic to you. Pink at baby showers means a girl, blue means a boy. This, while a "sexist" stereotype, is a cultural truth. We are taught the basics, and as our minds expand we can accept more abstract ideas. Homosexuality, for example, is an abstract idea. It defies not only rational thought, but the predetermined ideas brought on by our biology.
As much as you passionately try to fight it, these are the truths. Using traits and symbols with predetermined ideas attached to them is a key part of character design. If you want something to look scary, you color it black. To make someone look innocent, you depict them as younger with wider eyes.
Now, lets step back and reexamine the opening of the game. What we have established is the death and loss of a soul, but also a birth. We are taught by a mysterious figure how to feed ourselves and others, how to grow our own food, and how to defend ourselves. Does she not stand as a mother figure? Did she not call forth our soul and give us life? You are "birthed," and this the role of a female. If we tried to attach the idea of a male giving birth, this would require a much more abstract thought process. I know that might not hold true for all, but lets think generally here. When you were first born you emerged from your mothers womb and drank her milk. A common idea that we can all understand. Perhaps, one day, games as art will become more accepted and we will not have to use such simple logic, but for now we'll have to tough it out.
Now let us continue, with the idea that we are still a child. Is it not the father's role to establish order? Of course, this is not true for all households, but think generally here. The Brothers come in, they slap our wrists for misbehaving, and they teach us the "rules." We observe how they treat the Sisters, beings we have come to associate with life and love. We recognize an enemy.
Do you see how from just reading this description, even if I were to remove all gender references, you have reached an understanding of the opening of the game? Now pretend you are the designer. How would you sit down and try to establish a clear of level of consistency in the characters? The Sisters are mothers, they are female. In order to not blur the lines, so that the player can always recognize friend from foe, make the Brothers male.
I could go on, referring to how they feed the Sisters who create the new world (Did you seriously not read "SEX" in that sentence? Seriously?), but I don't have all day
However, does this train of thought make sense? Their gender roles are not assigned to them because the developers are sexist bigots, but because the characters display traits that can be easily recognized by gender.
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The shyest worm you can imagine