So I saw Civil War and while I've read the print edition, I didn't expect it to follow the print edition at all, I figured that they'd simply make this an internal rift between Cap and Tony, just like they've shown with the trailers. Obviously because the New Warriors weren't anywhere to be seen :). I think if you're going to make any big issue with any of the movie was that the villain that they were trailing in the beginning was rather wasted.
I think it's probably the most solid Marvel movie since wave 1. Winter Soldier was an incredible movie until the third act when it got super lazy writing all of a sudden.
I'd agree that putting Spiderman in the movie is... well, silly. And it stinks of Marvel hubris but it's not an issue in my opinion because he's there for fan service. While he played a big part in the print civil war, so did Danny Rand (as Daredevil) and you didn't see them doing anything with Daredevil.
But, I felt it was an enjoyable movie, and much better than most recent Marvel offerings, and at least someone finally said "You know, we've never really addressed the end of Iron Man 3, might as well pay it some slight lip service.