I can understand the criticism, as - when you factor in the main story by itself - pro-registration Iron Man and anti-registration Captain America veer greatly from their own character paths. Many point at Tony Stark suddenly becoming a tyrant and Mr. Fantastic playing God on the "Pro" side. I tend to believe the biggest seeming character veer comes on the other end of the spectrum as Steve Rogers - a "New Deal"-style Democrat - takes what is, on the surface, an extremely right wing point of view by going anti-Government.
However, reading the book again now - I find it completely voids most of those gripes. How? By pointing out in the material itself how out-of-character people are behaving. It's also worth pointing out how many decisions are propped up and expanded on in supplemental material... but I'm saving that for another review so we'll just keep the lid shut on that for now. (Preview: there are a few more books I think you should read.)
At this point it should be no surprise to you all that I like "Civil War." A lot. In terms of "heroes versus heroes" comics, it is without a doubt the best there is. Not so much because of what is happening, but the examination of why. To that end, Mark Millar leaves the main question open to a lot of interpretation. That being: who is right? While many people drift towards Captain American's perspective, and find him easier to root for, I can't help but reach the position that BOTH sides are wrong. One side more than the other.
Make no mistake, the biggest gaffe of Civil War is committed by the pro-registration side during the first real battle between the two at the chemical plant. But after that incident, I feel responsibility for the prolonged conflict falls on Cap's shoulders. Yes, Iron Man "started it." But Steve should have been smart enough to realize when it was finished. Instead, he pushes the issue even further driven to the point of insanity. When he snaps at Punisher in a late issue, you wonder which one is truly the nutcase. It's uncharted and uncomfortable territory for Steve for sure. Fortunately, Cap salvages his own character situation himself... just in time for his death in the pages of his own title.
Ultimately, this comic was huge for Marvel. It gave the Avengers the best exposure they had in years, divided or not and helped draw many people back to the medium. It is controversial for sure, and is practically required reading for good or ill. If you haven't... why wait for RDJ and Chris Evans (and Andrew Garfield too, maybe? Please? Pretty please, Sony?) to give it their own spin? See why so many people are excited about a film adaptation firsthand and pick this up pronto.