Civil War was a great book in that it brings up some really new and groundbreaking ideas in the superhero world, that really make sense and should have been brought up long ago. It's scope is nothing short of epic, and I think recasting Captain America as a rogue hero, leader of an underground liberty movement is genius. Just when they let the character shine for the first time in over a decade, they take him out of the picture. Fail.
Anyway, my main complaints are that the book was really repetitive. The characters re-iterated the premise and summarized each side every other page. Another weakness is tied to its greatness: the scope. The book was simply too short with the number of characters involved. Some of the major heroes got nothing more than a panel or two. Spider-man switches sides with almost no thought process shown in-panel at all. The whole thing just felt a little rushed and choppy.
I'm sure that this complaint stems from the fact that I was not immersed in the Civil War storyline for as long as it was around. I've seen that there are several accompanying books to the series and tie-ins that would add that missing depth, but I just wish they had collected it all in one place. I'd have paid more for it.
The ending is justly ambiguous and I'm eager to Wikipedia the Marvel Universe to catch up on what I missed since the end.