I might not be the only one who's said this, but I'm really bothered by the ethical imbalance in the Civil War. Supposedly, it's not good vs. evil, but come on! The Negative Zone gulag? Clone Thor? And look at the way Tony Stark treated Spider-Man. Tony acted like a father figure to him, while at the same time spying on him and letting Norman Osborn out of prison. Norman Osborn slept with his girlfriend, kidnapped the twins of that affair, killed his girlfriend, created evil clones of him, killed the only good clone who was basically SM's brother, and has shown time and again that he has all the ethics and respect for human dignity of a rabid dog. I don't care about those crappy nanobots that are supposed to control the Thunderbolts, that's just wrong. Tony also let out Bullseye, who murders for pleasure (including two of Daredevil's girlfriends). Have you read Choosing Sides? In it, Venom III is gleeful over registration because he's essentially acquitted of all his crimes -his murders- and allowed to walk free, attacking heroes again. Tony isn't just letting murderers out of prison and onto the streets, he's letting men who have killed innocents for pleasure and gone after the family and loved ones of heroes out, while putting heroes into the N-Zone.
That Tony is completely different from the Tony portrayed in the Sentry issue in New Avengers. The Tony in that issue was a man fighting for what he believed in, even though it was emotionally devastating him. He wasn't a man who would twist the Registration Act into an excuse to wrestle all the American metahumans under his fascist control, but that's how Tony is in most of the other comics.
It's like half of the comic book writers got a memo saying "Write an awesome yet heart-rending battle between best friends spurred by inevitable and tragic events" and the other half got a memo saying "Tony Stark is secretly evil and Reed Richards has been replaced by Super Skrull." Instead of Pro- and Anti-Reg, it's Pro- and Anti-Ruling-America-with-Clone-Monsters-and-Enslaving-All-Metahumans. I'm so disappointed.