LJ cut'd instead of comment-replied due to spoilers?
I feel like the ending was still true to the graphic novel. Sure, it was a little more contrived and a little less impressive, but it would have added at least a half hour onto an already long movie to get those parts in, and it would have felt awkward in a film rather than a graphic novel.
The pirate story I understand, though I also understand why they left it out. There's apparently a special edition DVD that's going to come out with it put in to the movie somehow? I'm not sure how they're going to do it, but hopefully it will be good.
Honestly, the part that I missed the most was how they had all these random characters that you really start to care about, and then they kill them all. Again, it's reasonable that they cut that part out of the film since the medium just wouldn't have lent itself well to it, but I feel like it was the most important part of the original that they left out. The millions of deaths weren't just nameless sacrifices; they were sacrifices that you had begun to care about.
Phew, that was long, sorry.