First off, Iron Man has always been one of my favorites and when RDJ started playing him, it brought Iron Man to life in front of my very eyes. However, just because you have an ability to do something it doesn't give any government the right to dictate when or if you can use your ability. I do agree with the point that like the rest of us, you need to be held accountable for the consequences for using them.
There is also the fact that criminals aren't going to register their powers. Why give "the man" an idea what you can do and where you are if you are going to use your abilities to commit crimes. Along with this, we all know that somehow criminals will get their hands on this database and either use it for recruiting or to see where they are less likely to meet resistance to implement their plans.
To me, this goes back to the government not trusting the people. President James Madison said: "Americans have the right and advantage of being armed - unlike the citizens of other countries whose governments are afraid to trust the people with arms." I think that superpowers are no different.