The problem with the current group of Marvel writers is that they're trying to create real world type stories in comic books. It's a trend that's been going on for a long time. There aren't just "good guys" any more, they're "real people" meaning they make all kinds of mistakes, to the wrong thing sometimes, and don't maintain their own character.
This is all done to make things seem more "real." The same is true of this whole Civil War story. Obviously, if superpowered people lived in the real world, there would be all kinds of laws and registrations, and whatever the government wanted to maintain order.
But this is COMIC BOOKS. For 70 years, heros have lived in a world where they operate outside the law. Sure, they have to deal with it, because they're mostly vigilantes, but part of the struggle with the heroes was balancing their "work" with their "life."
Peter Parker has been the ultimate representation of this. He views his responsabilites as Spiderman as not only something he's good at, but something he HAS to do, as he has great power, and therefor great responsability. He's also often seen as one of the most "real" characters. he has real life problems that he's always having to deal with. He has to deal with an unfair press, rent, college, a day job. He's not Bruce Wayne with infinite resources, or the Fantastic Four with Government assistance.
He's just a guy that got bit by a spider and does good things.
But back to my point. In the past, comic writers dealt with real life issues through allegory and creative stories. They didn't ask themselves... well, if this happened in the "real world" how would people react... becaust that's a stupid question... it's not the real world.
The current era of Marvel comics has all the writers asking themselves "if this happened in the real world... in today's climate (ie post 9/11), how would people react?" Well, it results in a whole lot of stories that make some sense if you ask yourself that question, but make NO sense with respect to the characters that have been around for 40 or 50 years...
They're trying to provide new ideas and new concepts to old characters... but they're using the crutch of "real world" scenarios to pull readers in, when in the past, writers would tell their own world's stories and leave it to the reader to make the connections to real world situations.
Couple of quick examples... The X-men dealt with Mutant-hatred throughout the civil rights era and beyond. They also dealt with the "Legacy Virus" throughout the era where HIV and AIDS were unknown and misunderstood. You can explore predjudice and fear without having your characters exist in the "real world."
It's fantasy.
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I don't know half of you half as well as I should like; and I like less than half of you half as well as you deserve.