Why are women extinct?
Without revealing too much, the women in Above the Catacombs were formerly second-class citizens and far less desirable than man in the work force. Although by 2030, most of the women still alive would not have lived long in a pre-war society - their numbers were far less than men. Gender imbalance is not isolated to fiction and is found in many countries throughout the world (India and China for example). Not to mention, most of the men in Above the Catacombs are middle-aged and their population is not too far off from extinction at 4.7 million. The mortality rate in Above the Catacombs is also expectantly high.
Furthermore, even if there were women featured in Above the Catacombs, you can certainly bet I would make them as undesirable as possible - like I did with the men in order to match the conditions of their environment. Maybe the criticisms were more related to a fear or dislike towards the idea of a society without women and or just a general misunderstanding. In our ever-growing sexualized globalist society that fights discrimination with discrimination, it would not surprising to find resistance to this rather male-centrist storyline - and yes, one of the reasons why I made women extinct in the story is to focus specifically on the chaste male characters. If our society is as "gender neutral" as it claims it is, then I would expect people who identify with opposite gender roles to find it no problem to play as a male character.
Personally I think a more sound argument, which has been brought up before against Half-Life 2 in specific, is why all the remaining humans seem to speak American English or why all the characters seem to be of the same height or why most citizens have pretty much the same eye colour; surely genetic variety would provide some diversity? You could easily say that due to technical limitations, adding that diversity would be more difficult to implement, but wouldn't adding a second gender be as well? After all, another gender just means more voice files, textures and models. In the case of Above the Catacombs, you would just need retextures, but that still takes considerable time and regardless isn't a good thing to try something different for a change? Not many stories...at least ones that I know of, kill off women - many forms of media rely on their presence - often an unrealistic presence by the way - to keep the attention of the audience.
Yes, in Above the Catacombs, all of the men are chaste, completely sexually abstinent. Some of them commit violence, much of it visible to the player, so it is not like the modification is attempting to be family friendly. Men in the modification certainly are distressed by the absence of women, but in no case are sexually frustrated. Unlike our own globalist society, they came from a rather brutal, but chaste one that only permitted sexuality in the context of marriage and child birth.