I guess a lot of the problems quite likely stems from making the movie for both LOTR fanatics and the 'normal' public. I never go to a movie expecting it to be like the book and generally try to take the movie as is.
The good points: I think PJ did an oustanding job of bringing Middle-earth to life. The Shire, Minas Tirith, Mordor, etc were done very well.
I agree with most of you that it was the treatment of a number of characters that I had the most trouble with. Tops for me was Treebeard (obviously). Next Faramir.
I too did not like the ghost scene on the Pelenor fields. Skipping
Tom Bombadil and the Barrow wights was OK. Only the LOTR devoted would likely have picked up that
Merry's sword was special and was the only reason he could inflict a wound so Eowyn could finish the Witch-king off.
Scouring of the Shire was a good part of the book. Gandalf sums it up by telling the Hobbits that setting the Shire 'to rights' was what they had been trained for. But the third movie was rushed as it was - although I would have left out the opening Smeagol/Gollum stuff which seemed to be done only for Andy Serkis.
The one little item I would have added because I found it to be rather amusing in the book was the banter between Eomer and Gimli over Galadriel. Just always found that funny, especially at the conclusion.
Just my two cents,
Chuck