Except the Boss didn't start out as some Overman, but was ret-conned into one in MGS4. MGS 3 portrays her as just another pawn in the game of the Super Powers. Despite all her skill, her will and her achievements she ends up sacrificed, literally like a pawn in a Chess game, when the USA decides it was the best move to make. That is at complete odds with Nietzsche's idea of the Overman, who would not be bound by common morality like "duty to your nation", which is the reason Boss gives for going along with the plan all the way up until Big Boss kills her (and sets the stage for his disillusion with service to a nation and gives birth to his idea of soldiers without nations). The Overman would certainly not be in service to something Nietzsche considered as base as politicians (who embody the oppressive masses that the Lion must rage against and rise above), and this makes the entire analysis faulty.
Not that I think the analysis was bad, necessarily. I just don't think Kojima understood Nietzsche all that well. Like many Japanese artists he has a fascination with symbolism and loves to apply symbols in his works, even when the meaning or philosophy behind the symbol doesn't make much sense in the context of the medium it is presented in. Kojima probably just found Nietzsche's quote really cool and felt that it fit with the "twist" in MGS V so he put it in.
