Basically the only gripe i have is him not doing the Scouring but i totally understand his reasons for not doing so since as you say the films are different from the books.
For me the Scouring is important because it changes the emphasis of the book from defeating an 'external' evil (Sauron) to defeating the 'internal' evil that lies within us all.
The films are the same as nearly all fantasy stories since Tolkein in that they end with the big finale and everyone lives happily ever after but the book changes that ending to an unexpected (for the hobbits anyway) and sudden jolt back to earth but which they then manage to overcome.
The Balrog is the best 'baddie' ever; the sequences were awesome. Hopefully PJ will do Smaug similar justice.