the interactions with the agencies, if he needed the contact influence from his GF does not seem very "manly".
so that is a bit strange, some times its just does not add up, some times is just better to assume power and corruption than to explain details too much details , but overall that is not bad.
to me the " He's just a stuffy, boring nerd " really pushes up when he does not interact or force any of the relationships with the girls, he is just too dam "Passive". you would expect the guy to maker some impression at some point so far he is a housemaid or something. no girl anywhere would be impressed by the MC actions so far, he is 99% pussy.
the girls look great , but the MC, he is terrible. its like he is "domesticated" / " dead inside".
What do the girls need to do to get some action, rape him?
and the girls have super powers and are fighting for their lives ( some are passive but not all ), someone needs to push their agenda on someone, normally that's the MC.
With all due respect, I don't think you have understood the game, like at all. First, the MC is some kind of legendary but already retired secret agent. Random active agents are not supposed to know his actual identity. So when he finds himself caught in this whole incident and there's already an agent working on the case who is only receptive to his official orders, the 'manly' thing to do is not to beat the shit out of that agent or to tell him who the MC is, but to covertly talk with the person who can actually let him work on the case too -who happens to be his former girlfriend's dad- and bypass that agent without confronting him. Not sure how you expect an expert secret agent would act in that situation, but what you seem to mean by 'being more manly' is probably not the way to go.
Then, it's obvious that this man still loves that woman, so it's only natural he rejects these girls who, by the way, are clearly influenced by their native world habits -when they throw themselves at him it's not because they actually want him, but because they've been raised that way. He's trying to calm them down, make them trust him, and also help them to adjust to this new world, and you just can't do that by making them your personal sluts from day one, because it would surely backfire on the near future. Again, it's not about being pussy or passive, but about being a smart and experienced agent, on top of a good man with a broken heart. His goal is not to bang them, but to protect them and the whole of mankind, too. The banging will happen, most likely, but it has to be slowly built on mutual trust and some actual care about everyone's feelings, not by taking advantage of this group of powerful refugees. That's the way he will impress them.
Now, of course, if you just disregard all of this characterization and plot and can only see a man living in a house with 9 hot aliens apparently willing to have sex with him, then sure, he's a pussy for not having had a massive orgy yet, or not even touched a boob after 2 days with them. But this is just not that kind of game.
Tho it's unfair you using the poor Sue for your mischievous intentions, who could resist those....eyes? Yep, eyes. Definitely eyes 
