Right off the top of my head, that whole business with the running-away-from-the-skull-avalanche scene just looks stupid; I can't believe they put such time and effort into it.
And also - they removed any sort of suspense over the ghost army, when he wanders out of a wall and says 'we fight' in a crappy money shot.... that is a truly on-the-nose example of when a filmmaker doesn't know when to leave something alone; when they feel the need to spell something out in ridiculous fashion.
Really liked LOTR for the most part, but for movies that people insist are the 'best ever made', there are a crapload of flaws in there. They are very much products of their time, and some shots will not age terribly well (that ridiculous shot of Legolas jumping on the horse, could've been straight out of Spiderman).