1) Changing of the personality/motivations of major characters.
2) Changing of major aspects of the plot
3) Changing of the themes of Lord of the Rings.
While I realize that Jackson is not directing the Hobbit (for which I am very thankful) I do not believe that most directors tend to be rather free with existing plots and characters, and they are moreso when they provide "filler".
If a second movie was produced, I would hope they would limit it to information on the third age taken from the Silmarillion and the Unfinished Tales.
The substance of the second movie remains a matter of conjecture and rumor. The reality of finances makes it certain that only a nuclear war has a chance of preventing its completion.