My opinion is that the dev overshoots a bit when trying to introduce the more esoteric elements of MC's character and add dimension.
His behavior with Mei for example is a bit odd. He claims that she is unique and brave because she is willing to stand up to authority, and then he says that he himself would never do it, when he obviously has no qualms being waaaay too casual with Elara and challenging her all the time, despite having accepted her as his commander, for better or worse.
Another example is that he seems to be affected a bit too much by the horrors of war which contrasts his overall character. Being a good soldier and being horrified by war are not mutually exclusive, but the way it's delivered leaves something to be desired and creates a bit of dissonance between the player's expectations and MC's feelings.
At times he seems way too controlled by his emotions. His reaction to Mei's injury is a bit over the place. He knows first hand that people die in war, he knows that Mei was the best candidate, that sending another Mech wouldn't save her, yet he can't help but blame Elara and the rest who accepted Mei's decision to sacrifice herself. Going to Elara and demanding to know the plan for retaliation is fine and in-character. The discussion with Lydia near Mei's tank however seems inconsistent to me.
On the other hand, I think people completely misjudge him. He may think that women are no good for positions of power and frankly, that's his perogative, but that doesn't really deter him from accepting his role and being fair. The way I see it, he has more trouble dealing with the complete absense of militaristic tradition. No protocol, no uniforms, no identifying insignias, lack of military discipline. This base is as chaotic as it gets and it's obviously frustrating to him.
He is also absolutely correct in thinking that this "utopia" is a facade which clearly evokes feelings of uncertainty and hostility. It's like joining a goddamn cult by mistake. People trying to persuade you that this is the best time to live on Earth while it's obvious that they barely believe it themselves. This world falls into the same patterns, while blaming the old world for it's predicament. There is still abuse of power, depression, classes of people, opportunistic behavior and the like. The difference is that the generation he lived in was more honest about it in comparison.
A small comment on the "femdom" routes and the relationships with the girls:
I think there exists some incosistency in the femdom routes. Getting drugged and raped, or being physically dominated by a mystical alien martial artist are fine. Might makes right. But willingly submitting to Mei and Sari seem way out of character to me. This man is outrageous and domineering in all aspects of his character. Allowing the likes of Mei and Sari to take control is bizarre and even if you play him as mild as possible, it still feels inconsistent. However the femdom content is obviously optional so I don't mind some catering to audiences that like it. I just hope that it won't devolve into a caricature, because despite his flaws, I like this MC and is something that isn't very prominent in the genre.
Similarly I think that the females are a bit too quick to fall for him. Valentina seems a bit repressed and Opal is thirsty as fuck so they are fine, but Lydia proclaming her love, Elara going from hate to love due to circumstance, Drana becoming his best friend despite her ideology and Sari turning from enemy to his little bitch seem off. Not that I mind too much, but the game goes from zero to hundred a bit too abruptly and heavily contrasts the prologue. However if it was to be reworked somehow, I'd prefer a prologue rework rather than a slower burn (duuh). Don't know what the dev is smoking, but I wish he would share with the others, because these girls are fucking bombshells, easily some of the best renders I've seen.
To close this, despite my (mostly mild) objections, I really like this game and eagerly wait to see how it will progress. The story is intriguing and the scope is epic. So the important thing is for the dev to continue following his vision and not be too influenced by ideological/unfair criticism.