I gotta say, having read the books, I was a little... confronted... by the size of Dr Manhattan's schlong when viewed on IMAX.
I mean, we're talking about 3 meters of glowing blue dick!
That said, I thought the movie was as good an adaptation as any comic is EVER going to get out of Hollywood. Of course you can't put everything in. It'd have to have been a miniseries, and then the production budget would be nowhere nearly as good. Ugly Betty costs something like $2m an episode, and it still looks like shit.
They still manage to have all the moral ambiguity of the books, and that's the point.
Ultimate good guy is the biggest psycho in history. The only guy that really cares about justice can't deal with doing what's "right". The only real superhero doesn't even associate himself with humanity anymore, and manages to have group sex with himself (oh, and a chick with a sweet arse).
It's all amazingly fucked up... Just like the books.