It seems like the super humans already are pretty regulated in this universe, so it's a different situation to begin with. Val & friends seem okay with the regulation so far, apart from issues regarding who gets to be a hero and who gets stuck being a sidekick.
And no, I haven't seen the movie, but I'm not planning to, so I don't mind spoilers. Just put them in spoiler tags in case other people DO mind.
True. The country has had the Hero Agency long enough for it to become mundane paperwork for the majority of the people working for them. After the first superpowered people were revealed, the government immediately went toward hiring them into the Agency. For the most part, it works out. You get to hero without being considered a vigilante, without cops and other citizens trying to stop you. Any damage that your powers incur during a fight is covered by the Hero Agency insurance. You are generally protected by civil and criminal suits and when you have to face them, the Agency has the best lawyers on your case. And they pay you a yearly salary as well as cover the rent for your apartment/house/secret hide out. Also, paid vacation and sick days as well as dental, health and life insurance.
On the downside, Val got stuck being a sidekick because she didn't meet the physical standards to be a hero as laid out by the Agency and there's little she can do about it without help from others and years of paperwork.
What I'm saying is that maybe there'll be some heroes who'll refuse to work with the Hero Agency and thus the Civil War-type battle royal!!!
I think the comic already shows that, and saying it differently isn't going to make this a Marvel tie-in. The system has been around long enough for it to be considered part of the culture and the way of system like the police force exists for us. Correct me if I am wrong, but it seems like the Vigilante is someone ("Hero" as far as I can tell) who doesn't participate in the agency, and thusly considered is a criminal. The full brunt of the established system has already shown this. You have to have a permit, sir.
Are you just curious as to what a hero vs. hero battle would look like? If so, I feel like there is a more straightforward way of asking the creators that.