First, a game does not need to work as an anime and have a defined villain through and through, it can have a hidden villain to create a mistery of sorts that lead players to wonder or in the case of this one, an anti-hero that leads the MC to some hidden agenda and wants said MC through some tough love to discover for himself what kind of hero he wants to be, meanwhile accomplishing her plans on the background, that is called later on a Denouement, that is when the nods of the plot finally becomes clear...
Second, the plot doesn't need an even more corrupt govt option because there is only one govt, it would need to be a 3th party or a outside influence, but H.E.R.O. already plays the part in the outside influence by being the "for humanity protection" front scheme, the govt itself even tries to recruit the MC, you don't need to understand who to root for or against, you need to understand with wich the MC has the most power later on wich i will explain in my subsequent points...
Third, if this is too much world building for you, i really don't wish to know wich 20 minutes completion time games you play on your spare time, because i have seen some detrimental world building and this is not it my friend...
Final point, there 220% didn't need to have a "Kratos / Alex Mercer" route because at that point H.E.R.O. wanted to boost the image of the now revealed identity of the MC to with that push foward their reveal as well and with an iconic hero to boot, and him facing Valran instead of the wind guy was a tactical move for that, to make the MC a true hero because lets face it, having an old man blasting Valran and half the city with it with people not even being able to keep up with what happened is not very hero like, with the MC as face of HERO he can literally overthow the people in power there later and be the head seeing that his kind occupies more than 90% of its man power and seeing as even the old man is unhappybeing there the way it is at the moment...
It seens its not the game that is giving you reasons to dislike it, you are the one creating reasons and expectations of what you would have liked to be in it that are really not.