I think you have to take the movies almost seperately from the books. They have to be enjoyed at their own level. Personally, although some bits of the films (normal and EEs) aggrivated me, I thought they were really, really enjoyable and skilfully directed. However, there's two things that truly annoy me about the films.
1) Saruman: in the books we know that Saruman is in fact a traitor to both the White Council and Sauron. Although in the movies he's obviously a traitor to the Council, to me the movies don't convey this, and he is portrayed almost as a good ally to Sauron.
2) The Elves and Dwarves don't seem to be troubled at all by Sauron and Mordor. Rivendell Elves are still free to go to the West if they want to, such as Arwen would in the movies, and this is utter nonsense. There was no escape for the Elves, Rivendell, Lorien and Mirkwood were all under siege (and the sending of aid to Helm's Deep, along with Elrond's visit to Dunharrow, was stupid). Also, we don't really see anything of the Dwarves.
The only clue to wider troubles in in the RotK EE when Legolas says to Gimli that war is already upon the Dwarves (or vaguely hints at it, really). This would be a perfect oppotunity for someone (Legolas, I guess) to maybe have a mini-speech about the brewing battles in Dale and Lorien, and showing us that, after all, this is not just a war of Men, as it is portrayed.
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