In fact, when I read the graphic novel, I skipped over "Under the Hood" and "Tales of the Black Freighter" segments when I got to them, and then went back and read them after I finished the storyline proper.
Perhaps, though, it would have worked better as two 2.5 hour movies instead of one 3 hour film.
My only complaints are that the director perhaps overemphasized the blood&gutsiness of the action sequences (similarly to "The 300", but on nowhere near the scale) and the actioniness of the jailbreak scene.
I definitely liked the film, though, and would recommend it to fans of the original work. Very much unlike the film adaptation of V for Vendetta, which I could not make it through in one sitting because of my disgust at how terribly everyone involved had missed the point of the original work.