Another change that I found slightly annoying: Anduril and Narsil, which goes hand in hand with Aragorn's state of mind. In the book, he was ready to be King and face Sauron, which is why he got Narsil at the beginning of the journey from Rivendell. And every time it's described how Narsil causes fear in the orc armies. I liked that.
Then, in Return of the King, I disliked how they handled the undead army and the appearance of the Black Ships at the battle of Pellenor. It's so AWESOME in the book, but the execution in the movie is lacking.
In the book, the ships arrive at the harbor, and the orcs are eagerly awaiting reinforcements. And then, suddenly, the ships fly the flag of Gondor. Then Aragorn, and 30 other Dunadain, jump into the battle. And Aragorn holds Narsil high in the sky, and it reflects the sunlight to make it look like it's in flames. And then Aragorn and Eomer meet on the battlefield, much like - in the new film - Dain and Thorin meet on the battlefield (I was actually really glad they did that).
The sequence in the novel is so cinematic. I can't believe they didn't include that.
Come to think of it, how they handled the confrontation between Gandalf and the Witchking also annoyed me. In both the theatrical and the extended edition, the confrontation feels badly edited into the battle. In the book, the build up and the confrontation was again much more cinematic. It happens right after Grond breaches the main gate. The Witchking rides through the gate, he is invisible, so you can see the fires of the battlefield burning through his metal crown. And Gandalf awaits him, prepared, not surprised.