It's really great now that we know that the director's cut will feature more of Rorschach. His origin scene, how he got the mask and more interaction with him and the psychiatrist. With this statement by Snyder I really hope these are all confirmed scenes for the director's cut.
Now I am really concerned about Dr Manhattan. Snyder tells that he was his favorite during the shooting and yet his scenes were simplified more than anyone's. Jon's flashback is a magnificent scene, and I doubt that it will be extended or changed, because of the editing with the music, but the thing with the picture must be extended (with I am holding this picture...) in the film we didn't truly realize the perception of time by Dr Manhattan. We, as viewers, don't get the feeling the same we get with the book, and I think with more editing that can be achieved. I really hope for that and the throwing of the gears, but Jon said about his father on the conference. I also hope that there will be more additional scenes with Jon and Laurie on Mars, and that his monologue to Laurie about the thermodynamical miracles will be extended as is in the book (but I doubt that also). I really hope for more scenes and more complicated scenes with Jon this time.
I think that Adrien needs more development and especially Bubastas. Since in the graphic novel there was a genetic experiment, we realize where Bubastas comes from, but in the film it doesn't fit well. Just one sentence will do the thing.
Hollis Mason's death is also one of the things we all know will get in the director's cut.
And definitely some additional scenes in the past, when they meet, and more Comedian interacting with Laurie, Ozymandias or Dr Manhattan.
Maybe Nite Owl's mention that Ozymandias stands for Ramses II in Greek, I thought that was a nice detail that was left out.
As for the Black Freighter and it's editing in the film, I don't have any idea how they plan on doing it. I don't think it would work as it does in the graphic novel, but it would certainly be interesting to see how that plays out in the end.