Riverrun covered that very well, and I don't think I have any complaints about what he said. However, (here it comes), the biggest change to the film is at the end, 10 seconds from the credits. In the original, when Willard and Lance are pulling away from the camp, Willard calls for the air strike. In Redux, he doesn't!

What does this mean?
We are not only deprived of an amazing closing scene but the assurance that Willard is the good guytm. All of the way through the film we see a messed up assasin go from thinking the target is a raving loony to a great man. We see his thoughts more clearly as we listen to the narration in the camp. He even states that he doesn't belong to the army anymore. That is in the original, but now it makes more sense.

Why does he kill Colonel Kurtz and leave the camp?
Because he was ordered to. Kurtz goes from asking if he will kill him to saying that when he does, he must tell his son his achievements. We even hear the Colonel say that he hates all of the lies, something Captain Willard has already said. This last change reinforces this idea by not letting us think that once he killed Kurtz he was somehow cured and had gone back to his duties.