The highlights of the ride for me are the two "extended" mood pieces involving the cave and the wharf. On paper they probably seem like unnecessary digressions and I wouldn't be surprised if some of Disney's people argued for a more consistent, more story driven approach. Walt was right, though. The best rides are about mood and subtext.
There's a poignancy to it, a feeling that the world is staggeringly beautiful and full of menace at the same time. For me the periodic displays of skeletons and pirate loot are just icing on the cake.