It is often the lighting and the motion in the scenes in LotR which hide the obvious cartoony look associated with cg. Just look at gollum, he looks really cartoony sometimes. And the digital doubles in scenes don't really look better in this either, like in the legolas shots.
And what else was george supposed to use miniatures for in the prequels? He used them as much as he could, I don't know where else he should/could have used them.
And with the clones, I never knew they were digital in Attack of the clones until I found out they were. The thing that makes the clones look cartoony is the way they move. The actual digital models of them are very good, especially in episode 3.