First of all: Team Cap all the way!! No question about it! But why, and how these same principles can affect your RPG: (This is all based on the movie and not the comics. No spoilers!)
First - Team Cap represents personal responsibility, not rule by the Nanny State. Team Iron Man is all about letting other people tell you what to do, but Team Cap is freedom. I think the Watchmen showed us what it’s like when “supers” do the government’s bidding, as did Martial Law. Cap is right - He cannot allow himself to be controlled by the UN and allow them to dictate what he can and cannot do. Let’s be practical here, the UN has Cuba, Nigeria, Russia, Saudi Arabia, and the UAE on its “human rights” council. Are these the people who should be deciding when it is a humanitarian effort to go and save someone? (I know, it would probably be the security council, but they don’t seem to have any obviously stupid members at the moment.)
Second - Iron Man is an ass, and not in a good way. Sometimes you need a real @$$hole to make decisions, because they can make the tough calls, but the mere fact that TBolt Ross and Tony Stark think it’s a good idea is enough reason not to do it.
Lastly - Trying to avoid spoilers, even though you should all know this stuff, but ... Cap’s team is fighting for someone that they all know is effectively innocent. Getting angry at him is sort of like destroying a gun after an evil person has used it. The gun was not at fault and had it not been for that gun, the evil person would have found some other way to do what they wanted. So getting pissed at the innocent is what we do now?
How does this affect your game worlds? First, there is a difference between a soldier and an adventurer. Adventurers are far more mercenary. They follow far fewer laws and social conventions. They do as they please mainly because they can. And governments (and others) find them useful for this reason. Just like we still use mercenaries today. Oh, I’m sorry, paid military consultants.
Soldiers are different. Typically you need to convince them that they are right. There are a lot of soldiers in history who chose not to follow orders when they felt those orders were morally wrong. Yet there are a lot of soldiers who did things that today we see as evil, because at the time someone convinced them that it was the right thing to do. With all respect towards our fighting men and women, they are rarely given a choice about the morality of the conflict, but that does not mean that they have not been convinced that it was good or just.
So Team Iron Man wants to actually be super soldiers, but Team Cap (who is the “super soldier”) recognizes that sometimes an army is the wrong tool to use. I believe strongly in personal responsibility and personal freedom. I am actually pretty libertarian in my political views and typically feel that those who do no harm to others should be left to do as they please. I get that Team Cap is ready to take responsibility for what they are doing and make decisions on their own. If Cap kills someone, he should be held responsible. If someone dies while Cap is defeating a wild robot bent on murdering every human in the world, well as much as I may grieve for the families of the fallen, Cap just saved your asses, and gratitude may be the right thing, as opposed to a civil lawsuit.