It has been a long time since I played this or read the books, but from what I remember:

Books four through seven go into detail about the culture of the Patryns and Sartans, showing that they are more complex than simply the forces of good and evil. Everything from book three to the middle of book seven is cut out of the game, so none of this is shown in-game.

Zifnab changes from an insane man rambling about pop culture to a powerful, sane wizard at the end of both versions. This happens because Haplo uncovers his past and helps him regain his memories in the books, but is inexplicable in the game.

Sartan coffins are found in the dwarven island in both versions. These foreshadow the fact that the Sartans have been using their magic to assist the islands in the books, but goes nowhere in the game.

Haplo saves his former master's soul at the end of both versions, which shows in the book that he has come to accept that the master's actions were morally ambiguous; but in the game, he had just been betrayed a few hours earlier, had found no reason to trust him, and so doing that made no sense.

Someone who has a better memory of this, please comment.