I thought Dr. Manhattan and the Comedian were both pretty compelling characters. Any alternate history in which "Some time in the 50s a dude who could do pretty much whatever he wanted started existing in America" is a premise is gonna seem far fetched. As a whole though, the way the story is told admittedly has a lot more merit than the story itself, which is why the movie was for the most part inferior to the comic.
Dr. Manhattan and the Comedian had the merit of not being complete freaking abortions, but I didn't really feel that interested in either.
It's less that the alternate history was far-fetched - you sort of expect that in a comic book, although I kinda got annoyed that some things were changed "just because" and some things weren't changed at all even though they probably ought to have been - but that it was so transparently a vehicle for Moore's ideological declamations on the Cold War. I mean, Nixon a dictatorial President-for-Life?
Really? Also, it seems to me that it wasn't Manhattan's thing that was "the" PoD, but something earlier, connected to the rise of costumed vigilantes in the United States of the thirties.
The storytelling wasn't awful, but it kept getting bogged down in trying to do entirely too much at the same time. Juggling the stories of the thirties heroes, the sixties heroes, Jon/Laurie/Dan, Rorschach, that trippy pirate story, what passed for high politics, and of course the main Ozymandias plot got too much and I felt that they only managed to do justice to a few of them, while the others unnecessarily distracted - although given the weakness of Ozymandias' plot, I suppose that might've been a plus. The variety of the materials used to present the information was interesting, and the liberal use of flashbacks was somewhat innovative for the comic books of its time, but neither of those things made up for the overall weaknesses of the story.