I just think it goes on for too long, and there are a few aspects of it that I think go directly against the established history of the Watchmen universe, such as the picture of the "Watchmen" (Crimebusters in the GN) being taken when they never actually formed a group, Dr. M on the moon (a "WTF?" moment for me), the Comedian killing Kennedy (hinted at in the GN, but you're never sure if the Comedian is just joking or telling the truth), and the prominent featuring of the lesbian Minuteman (Minutewoman?) whose identity and purpose are never made clear throughout the rest of the film ...
I may trim it down (the credits are 6 minutes and the real song is 3 minutes!) and keep it, but it's most likely going to go.