I don't know what the timeframe is they're working in, but I guess she felt she had to add some duress to 'awaken' Yuya to his potential.
I guess the only real question mark is why he's the only one being primed for what I presume will be the new TSF they're going to use to take Japan back with. I mean, what's the point of the other three members of Argos, then?
Also, I imagine every military force has a 'special' class. Delta Force and the SEALS for the US, as an example. That's nothing new.
Anyways, based off the pacing, and if this is really only 12 episodes long, it appears we're not going to return to the real battlefield until the climax (last 2-3 episodes presumably), where they presumably go and (attempt to?) retake Japan. I'm a little disappointed, after all the action and angst of the first two episodes.
I guess it's turning out to be more Top Gun, and less...I don't know...Platoon. Not that there's anything particularly wrong with that; I was just hoping for more actual BETA fighting.
Edit: The soldier vs warrior thinking outlined above is outdated, imo, for the real, modern world. That said, if I existed in this fictitious Muv-Luv universe, where you've got hordes of rampaging aliens that are nice enough to zerg en mass everywhere they go, the last thing I'd be doing is concentrating on small, elite forces, and the very idea of putting people into what I can only presume are hugely expensive mecha-regardless of their design philosophy-to fight off these zergs, would make me cry at the absurdity when looked at through a cost-risk-reward lens.
But, as a piece of fiction, it has the benefit of not having to make any sense, and just needs to entertain, and it's doing just fine in that department, so /shrug.