You know, I think I would not be interested in seeing a Civil War adaptation. Sure, okay, the issues of security vs. freedom are worth exploring in this day and age, but I really have seen enough of heroes fighting heroes. I can buy the idea of heroes initially being at odds due to a misunderstanding or difference of priorities, but ultimately their shared commitment to heroic principles should enable them to move beyond that and realize they need to work together. What was cool about The Avengers wasn't, for instance, seeing Tony and Steve bickering; it was seeing them instantly put their differences aside and work together the moment danger struck and lives were at stake.
And I agree, it really is hard to see Tony Stark buying into the government's pro-registration line, especially in the extremes to which it was taken. That felt out of character to me. I recall there was a lot of inconsistent characterization in and around the Civil War event due to all the different writers not being on the same page. It seemed that characters were forced into actions and attitudes that they'd be unlikely to support just in order to drive the story. That's not something I want to see in the movies.