We've come to expect certain things from our RPGs, and the ability to save anywhere is a big one. So is some element of choice, even when it doesn't have a major effect on the story. However, the biggest is the ability to decide our avatar's gender during a character creation progress. If we're able to decide everything else about our character, it only stands to reason that we could choose whether it is a he or a she.
Which is why it would initially seem odd that South Park: The Stick of Truth, a game that gives us so much control over our character's appearance, would make every player male. However, while it may seem like an issue and something we should question, it really isn't. In fact, the gender of the New Kid doesn't matter at all.
For the sake of the story, yes. The New Kid is male. Trey Parker and Matt Stone had a story in mind, and the gender had to be set for certain elements to work. Without getting into specifics, one of the storyline quests on the third day involves pretending to be some girl's boyfriend. Despite that moment, and a few similar ones, players aren't really forced to think of the New Kid as being male or female.
We are given a wide variety of character customizations, after all. Though my New Kid started out looking like a surfer with purple hair, it didn't last. New wigs and makeup options are everywhere. It wasn't long until he started looking more like a she. First, there were the (pink) pigtails and some rather awesome glam makeup. Then, after doing some shopping, I switched to a tasteful Lolita wig and blush. Word of God might say the New Kid in general was a boy, but my avatar certainly had some feminine wiles. There were even times I forgot he was a boy, because he just looked so goshdarn precious.
Not only that, but it's even easy to forget the actual gender of the New Kid. Aside from the occasional male pronoun, he's always referred to as the New Kid or Douchebag. Both nicknames are relatively gender neutral. The same can be said for the nicknames the avatar's parents use. Endearments like "Champ" are more commonly applied to boys, but could be used to refer to girls as well.
Even the storyline missions themselves seem to encourage vagueness. Yes, there is the aforementioned moment where the New Kid has to pretend to be someone's boyfriend. But aside from that one storyline quest, nearly every other action and quest relates to something both men and women could do. It's almost as though Parker and Stone were intentionally leaving some elements of South Park: The Stick of Truth ambiguous. Yes, the New Kid is a boy, but his gender isn't really forced on us.
Honestly, I didn't care what his gender was. I've been playing RPGs for over 25 years now. I'm used to using male avatars, even though I prefer to play characters who are more like myself. But, with South Park: Stick of Truth, it just didn't seem to matter. Yes, his gender is stated, but the New Kid is an absolutely blank slate. You determine what he looks like, he's a silent protagonist, and practically every nickname used isn't gender specific. If someone really wanted, they could probably even pretend this is situation where a tomboy is repeatedly mistaken for an actual boy.
The fact that such a thing is even possible proves that, in this case, the avatar's gender doesn't really matter. Slap on the appearance altering accessories that make the New Kid look however you want him, or maybe even her, to be and go fight some aliens and underpants gnomes.