I think on a fundamental level we agree: super-humans can cause much more destruction than regular humans. There should be some accountability to the actions they perform that may endanger innocent civilians. However, I think there's some nuance that is not completely discussed and some misplaced trust in the government.

One of the biggest issues I have with the Super-human Registration Act starts making it an "us vs. them" issue, rather than just a national issue. You're already antagonizing others by making it seem like they are doing something wrong or they will do something wrong simply for having super-human powers. It leads discourse to be a conflict rather than an amicable discussion. It also adds mistrust and suspicion when dealing with strangers and friends alike. This is an act that divides people rather than an act that protects people.

The government also acts on its own behalf rather than the people's. As much as the government claims to protect its citizens, acts such as communist hunting, wars on drugs and terror, and more recently SOPA and PIPA have shown that the US government's much more concerned about control rather than the well-being of the average citizen, although this isn't exclusive to the US. I'd also like to add that much more often the government will act on the interests of corporate lobbyists. It's why copyright law is so outrageous and why drug companies can directly advertise to the public with commercials. I believe there's only one other country in the world that allows this: New Zealand.

But I digress. The US government already tracks us and records as much as it can of its own people. They say that they've collected so much information that they cannot possibly read through it all. But they have it. And if they have it and you do something that raises their concern, they then have a backlog of whatever actions you've done in the past. They do this to everybody, not just those deemed "dangerous."

If you give the government the ability to track or even possibly hunt super-humans without any repercussions to actions it takes, that gives the government much more power to take out anybody whether warranted or not. You've already given them targets to observe. Even worse may be if corporations were able to wield its power to make it possible for them to capture or experiment. As much as I would like to trust the government, history and current events have led me to think otherwise.

I only thought of this as a real-life situation rather than the Marvel universe, though the issues I address should be problems with any government similar to the US.