If the basic blueprint for Civil War is " SHRA passes in wake of metahuman tragedy, inspires massive panic on all levels ", then I'd make the following changes...
-- The heroes are freaking out about the SHRA's existence before it passes. The X-Men are well aware of it, since it predicts a Days of Future Past scenario ( remember, in the original story, Kate Pryde recounted how the Sentinels killed all the non-mutant superheroes as well ). The Avengers are aware of it, but their reactions vary greatly; none of them wholly agree with it, but some don't see it as a big deal a 'la the America of Sinclair Lewis' " It Can't Happen Here ". The supervillains are going utterly nuts about it. The second the news hits the underworld, there's a widespread villain panic, and well-intentioned extremist bad guys ranging from Magneto* all the way down to Firebrand are getting more and more desperate. Heroes fully aware of the ramifications of the event like Iron Man don't entirely disagree with the villains on the issue, and they're getting more and more frustrated.
-- The circumstances of Stamford are much more complex and suspicious. This would not be a case of ill-trained New Warriors taking on a bad guy out of their league; in my version, we'd get mutants ( the catch-all persecuted minority for Marvel events ) as the heroes who fail. I'd imagine it as a squad of the X-Men student class running off to take down Nuke, and being obliterated in the process. The fact that it's mutant scapegoats ( similar to how 9/11 scapegoated Muslims ) makes the X-Men the first to receive blame; the other superhumans actually come to the X-Men's defense, and the result is that superhumans at large are targeted.
-- Tony Stark's role is radically altered. Instead of immediately joining with the bad guys without even trying to beat them, Tony's the one who smells a rat. Tragedy and civilian casualties are nothing new in his line of work, but this seems orchestrated. There's too much coincidence; why would the heroes, even young and impetuous ones, manage to even get near Nuke ( who's probably on multiple SHIELD Most Wanted lists )? Why would Nuke be hanging out near a schoolyard? Why are the records for Miriam Sharpe, the first sympathetic parent figure to come forward, so nebulous? Tony spearheads the charge to find out the truth with a level of fantaticism not seen since the Armor Wars.
-- Cap's role is changed, because while Iron Man plays the bad cop who breaks fingers for information, he has to be the good cop. Cap's trying damage control for the public, trying to use his patriotic messiah status to return favor to the heroes. He's not terribly successful with it, and he's cracking up in his own way; how can his country be responsible for allowing this to happen?
-- The change in the villain/hero dynamic that occured in Dark Reign happens here; the heroes are on the run from the law, and the villains get jobs. But since it's too much of a stretch even for Marvel to think that you could make Venom into a beloved children's toy, the villains are repurposed; instead of just being given nano-chains, their free will is basically erased. They're effective zombies, expendable troops targeted at the heroes.Â
-- There is plenty of hero-v.-hero strife, but it's not a heavy-handed political allegory so much as breaking from the stress. The Fantastic Four face internal dysfunction because the Richards kids are targets as well, and being on the lam is no place to raise a child. The Avengers' make-up is shaken by the fact that a lot of the heroes don't want to defend a public that fears and hates them. And solo heroes like Spider-Man face the worst difficulties ever; a " Marvel Knights " arrangement of urban heroes forms out of necessity, even when it becomes more and more apparent that they can't work together.
-- The story resolves with the X-Men leading the charge against the SHRA. Before, they were the outcasts while the other superhumans were treated like royalty. Now that all of the genetically abnormal individuals are targets, the X-Men are the ones with experience as being the rebel force. This is a turning point for the mutant stories; they finally start to get the recognition they deserve, since their courage and skill is noticed now that the playing field is level.
-- In the end, the SHRA is repealed, but there's quite a bit of damage to repair in terms of public perception and personal trauma. And there's no crossover immediately following this one...