I think you aren't separating "in Eternum" vs in the "real world," and I think you're missing some factors.
In Eternum he is level 1 and everyone but Penny and Nancy are much higher levels than him, that's why they out do him there. In the real world he stands up to Axel, the modeling agent guy, and a bunch of other things he can do. But yeah, irl they are all pretty normal, as you'd expect.
It seems like most of your issues come from things that happen in Eternum where he is weaker because he's the third newest player. But even there he preforms well, he beats a champion gladiator, survives an alien takeover a space station, takes on Thanatos, solves puzzles and mysteries, and a lot of problems and he gets the team out of issues just as much as the girls do for him. Especially if you, the player, make the right choices.
That bring us to Nancy, as Penny has never done anything that has been "emasculating" to the Mc in Eternum or in the "real world." But Nancy really doesn't do anything herself. She punches one guy, after Orion kills the guy's champion, and because that guy was a dick another guy just declares her the Empress because she promises him weekends off. Nancy in the "real world" is an older, smart, accomplished manager, and she's basically playing a management strategy game while in Eternum, she isn't doing anything herself but using the people around her to the best effect which is just her IRL job, management. With the exception of killing sirens in the latest update that is. And with Orion's powers, the girls high level, Calypso's powers, Nova's weapon, and such they do really well under her management. Having the girls be competent doesn't invalidate Orion's competence and he is the linchpin of the whole thing anyway. The dude stood up to Thanatos after being stabbed in the chest and has surpassed most of the girl in raw power in a shorter time starting from nothing.