What were Marvel's heroes fighting about during 'Civil War'?

I don’t know if the movie version of Civil War will follow the comic version as I don’t know what everyone will be fighting over. The miniseries from 2006 basically concerned the conflict over whether people with superpowers should register with the government.

I never read the full miniseries because I got disgusted and dropped it but here’s what I know about it. As part of a reality show, the young superhero team the New Warriors had cornered a bunch of villains in Stamford, CT. There was an accident and the nuclear-powered criminal Nitro exploded, killing a bunch of civilians, including nearby schoolchildren. Many people blamed the heroes and argued that heroes should register to receive training in the use of their powers and in some cases, the government should conscript them.

Leading the pro-registration side was Iron Man, who found allies in Mister Fantastic, Hank Pym, the Wasp and Ms. Marvel. On the other side were Captain America, the Invisible Woman, Luke Cage, Hercules and the Falcon. Spider-Man unmasked and defected to the anti-registration side. The X-Men were neutral. 

Apparently, the writers meant for the readers to side with the pro-registration side but this backfired because Iron Man and company were acting very authoritarian. Civil War led to some ugly or stupid scenes, such as SHIELD ordering soldiers to fire on Captain America, Iron Man cloning Thor and the clone killing the hero Goliath, and a reporter lecturing Cap — who punched out Hitler on the cover of his first issue — for being out of touch with America because he didn’t watch NASCAR or go on MySpace.

Most risible was Reed Richards’ explanation for his pro-registration stance. His uncle had refused to name names to the House Un-American Activities Committee in the ‘50s and Reed sided with the HUAC because while he didn’t agree with the anti-Communism circus, he thought his uncle should obey the law. Reed Richards sided with Joe McCarthy over his own family. I can’t believe anyone could write that and expect to see Reed’s point of view. Sue certainly didn’t and left him temporarily over this. Oh, also, Reed and Iron Man built a prison in the Negative Zone for heroes who refused to register. So there was that.

I was firmly on the side of the anti-registration forces. Marvel has always had a laissez-faire approach to organizing its heroes. The Avengers and Fantastic Four would cooperate with the federal government and SHIELD but maintained their independence. The X-Men, especially Magneto, always fiercely resisted any registration of mutants, rightly fearing that it would lead to internment camps (as it did in Days of Future Past).

Readers also pointed out that during the ‘80s in Fantastic Four, it took all of one issue for Reed Richards to convincingly debunk the argument for superhero registration. I don’t know why they needed a seven-issue miniseries and multiple tie-ins to rehash the whole thing.

There’s an argument to be made for training superheroes so nothing like the Stamford massacre would ever happen again. But I don’t like the effect of the program that there were 50 Avengers teams and everybody joined. I think the Marvel Universe works better when there are unorganized, Wild West pockets of mysterious heroes who come and go.

Civil War was so joyless that it distanced me from Marvel. It kicked off a period when heroes didn’t defend Earth from villains or saved civilians from harm. They all just argued politics with each other and I had no interest.