After watching the Ms. Male Character video (from series Tropes vs Women in Video Games, https://www.youtube.com/watch?v=eYqYLfm1rWA) I've come to the conclusion that not only as the author notes the trope originates far deeper in the culture than the video games (biblical Adam and Eve story is mentioned), it also cannot be resolved at the level of video games, because those only reflect the culture itself.
Obviously the problem has several layers, one of which is that gender and sex are still interchangeably used. Sex is a biological aspect of a person and is by design binary, while gender is a social construct intended to capture (behavioral and other) stereotypes. Therefore although having a specific sex predisposes a person to certain behavior and thus genders, this is not absolute - a person of specific sex can be of an improbable gender. Since in the most situations the sex of a person cannot be observed (or rather validated), we fall back on differentiation on the level of gender.
General effect of this is that the genders that are represented in video games reflect their visibility in the “real world”. The lack of characters in video games, who are not of one of the major genders, is exactly because they are in minority and therefore it is tough to faithfully represent such characters. And even then the creators are likely to be criticized for some specific behavior of the character misrepresenting it's gender as if the point isn't to avoid normalization. This is quite obvious even as characters who are typecast as women are included in the games. The creators, being predominantly men due to the imbalance in STEM fields, struggle with accurate portrayal of women, obviously even more so than professional writers.
It should be no surprise then that the video game creators fall back on the stereotypes that they know, because simplicity is the major reason why gender labels exist (as is true for all other labels/concepts). One of the repeatedly mentioned distinguishing elements is a pink bow on the character's head. I would say that this is because outside video games this stereotype still holds. In the “real life” the way you can guess a person's gender is to watch for typical signs of various genders. For women those are secondary sex characteristics, clothing, hair, nails. Different people look for different things, but the general understanding is, that hair accessories and high heels are reserved for women. Therefore these are used by women to signal to other people what gender they associate with. I don't think it's particularly reasonable to expect the video games (most of which are intended to bring straightforward entertainment) to push the socio-cultural evolution. In the end they are for-profit efforts and very few studios have the track record to afford this kind of gamble.
Another curious thing is that while the idea of gender equality seems like something that should enjoy general support, the word “feminists” still represents a minority subgroup of “women”, even though it should under this assumption refer to a large majority of population. This aligns with my personal observation that gender issues including gender equality are something that most people want to ignore or they actively resist understanding. There are two reasons I see.
Most people like the simplicity of binary gender roles. From their point of view they belong to one or the other and the rest of it are just unnecessary complications. And this is a completely valid point as people with unusual gender or unusual gender preference have more trouble finding a life partner. This is not likely to change as it is based in biology as opposed to psychology (search for “homosexuality is not a choice”).
The second reason is that historically the current gender role stereotypes are so deep that neither men nor women are willing to give up the advantages that this brings them. For men the first that comes to mind is higher pay. This is however so entrenched that some research has shown (can't find the link now, consider this unverified) that both men and women expect the man in the relationship to have higher salary than the woman. What I however consider disturbing is that many women I know, expect men to be less aggressive and more aggressive at the same time without realizing it. Equal pay and equal division of housework (men less aggressive) is a very popular idea among them, but they effectively opposed to any improvements the gender equality would bring to men, like they don't initiate interaction half of the time (forcing men to be more aggressive). Another baffling example is so called chivalrous behavior - many women expect it, but I don't see any way this doesn't directly undermine equality.
It would be nice to hear from members of opposite sex or non-man gender what characteristics they use to determine that a person is a man or male. Maybe there are also tropes for men in video games that are not immediately apparent because men are the expected default.