Captain Jack is still a glorious cowardly dick.
I do understand where most of the criticism is coming from, though. It's absolutely not self-contained. There are a ton of plot strands dangling all over the place. And Marc Singer's (no, not that Marc Singer) criticism of the treatment of nonwhite characters is hard to dodge.
I don't agree with the people who say that Commodore Norrington's behavior was strange, though: they establish that his life had been ruined because he did the right thing at the end of the first movie, and he was understandably bitter.
I did think that the ending (such as it was) dragged a bit. It was the only point of the movie where I was actually thinking "Come on, get on with it" (the rest of the time, the frantic action covered up the fact that the story had stalled out). It felt like, after the last battle, they should have wrapped it up pretty quickly to set up the next movie, and rolled credits. On the other hand, the final twist is an Oh Shit moment.
Stay through the credits. It's worth it.