So in your context, the superheroes would be the service folk? What is the flawed system? Just having dumb people in power? cause we can agree there.
It's easy to lose trust in police/firemen/doctors/superheroes when you hear your whole life they are there to save people, but miss you when you need them, but we simply can't save everyone. Saving some is better than none, hopefully that "some" will eventually be everyone, but that's something """""""""we"""""" have to work towards.
I do think the limitation of manga as a whole is that every ideaology has to have a character representing it, its the same problem with the xmen and mutants as a narrative trope. They cast a net too wide which lets them touch on many points, but ends up as a flawed analogue to whatever they do choose to make the condition of mutant, in this case hero, with. So to answer which one is to say all of them.
And i'll make the same recommendation of read literature that allows the abstraction of the concept speak volumes about the depth of what they try to discuss Those Who walk away from Omelas by Ursula K Le Guin.
And im not trying to make pontifications or arguing with you, hope it didnt come off that way, but its more so an ailment of trying to solve any issue, it inevitably divides those who have and those who have not. If a system has more interest in drawing those lines instead of, as you said, having it encompass a wider net, should that system be reformed, over turned, or refined.
To keep it in the scope of fiction, id think Goat is of the mind of reforming, the assassins are in the group of refining, the heroes probably dont have much of a say in what their day to day tasks are beyond "keeping the peace", and the outcast kids are of the mind of over turning the system. The issue being "keeping the peace" costs the lives, by their perception, of the outcast kids.
Therein lies the real world analogue, what systems in our world cost a price that we cannot see but would not be passable to our own self-interest/moral compass? How deep does one need to trace that line before less cruelty is enough, and even then that less is someone elses red line and so conflict is inevitable unless something drastic changes in the earlier chain. In the fiction that's Goat's main conflict, what is his redline, and can he come to a decision before it's made for him.