You have to learn to recognize peacock by its feathers. (<-I know the actual idiom is different, but I don't care.)
This is basically the same as Isekai genre, ie. male-power-wish-fulfillment-ego-stroking-fantasy.
The signs are all here:
The MC is OP.
Slave waifu, who is super supportive...
I think, this is intended concept of this manga, but there is skill issue on the author's part. Like a @ziomatrix says above, the setup is fine, but the execution is extremely clumsy.
This.
The whole "Guys don't cry! Be a fucking man!" mentality is not about crying per se. It's about the fact that as a Man, a pillar and protector of your family, you are supposed to be strong-willed, dependable and not crumble at the first sight of problem(s). You fight, you die, but you die...
Vysis is pragmatists to a fault, so pruning the students, which could/would become liability in the future, makes perfect sense for her. Also, she let it slip because Sayaka was disobedient to her from the very beginning and sort of failure among the S-ranks, so letting Sayaka killed while...