Civil War as it was written suffers from two main flaws that are easily fixed, and one that takes a bit of editorial courage.
First, everybody was written like your standard Mark Millar ******* protagonist. Not having Millar write it fixes this.
Second, you need to add an actual villain everybody can put their differences aside over, who is behind a lot but not all of it.
Thirdly, you need to admit that Stark's position of holding superheroes accountable for their actions is sane and Captain America's position of vigilantes being allowed to do whatever they want is lunacy and not have Stark go nuts to make Cap look like the better choice, and end it with (a variation of) the Registration Thing being the new status quo and everybody except lunatics like the Punisher being more or less okay with that.
(Or just do what DC did with the same story concept on Kingdom Come, and make it an out-of-continuity story)