I understand what u mean. The story didn't get me as well. Sometimes the suspension of disbelief needs to be too high because it's a porngame + sci-fi themed. I don't have a problem with this at all, a sci-fi theme gives Stiglet more freedom to create different events and explanations, but this war mistery was kinda lame (that's the only poor side of this game for me).
Maybe the girls don't display the war circunstances on their faces because this specific ship is not a battle/war ship, so, they are not involved in this war directly. Also, the war is older than all girls, this is reality since they were born thus not enough to make them live depressed around the corners. Finally, they represent hope for humanity as a colonizing ship and all of them are volunteers, both determinant for mood.
MC is not the last guy on universe, but I supposed since the beginning that if humanity is losing the war and military forces are mostly male, men are in smaller numbers than ever before. Also, the crew is 100% female and this is enough to elevate the sexual tension even between them. That's what I translated from all the flirting and overwhelming simpathy, but this could be better explored in dialogs.
I would say that MC's motivation is to be useful for the mission and crew. I don't mind that he is not special in any way yet, this can be explored/developed in the future, even more in a sci-fi game. As for the girls, I don't think they need to be rewritten. They have different reactions to the MC that match their different personalities. The girl who grew up on an asteroid is visibly more naive than the others (she thinks you're looking to her crucifix, she accepts that the explosion accident was her fault, she gets blushed when you find her vibrator). I would make just some minor text changes and additions, mainly to the war plot.