Spoiler Warning....Spoilers To Follow
Well, the major problem with the novel (for me) was Stover's style. It really bugged me. Right in the middle of important things he would suddenly stop and go off on this tangent about events and things that happened outside of the movies. It mostly struck me as EU stuff and I really didn't care about it since I don't read EU. It was like he was trying to fill up pages. I wished he'd just stuck to the story and left EU stuff to EU. Thus, I found myself rather bored in spots.
Also, I hate to be the bearer of bad news, but this novel didn't tie up everything with a big pretty bow. There are still things left unanswered in both trilogies and there are even new plot holes opened up. Like that's a surprise.
According to the AOTC DVD commentary, George states that who erased Kamino from the Jedi Archives and why would be revealed in the next movie. Well, it might be in the movie, but the novel never even brings up the subject. Nor is it ever reveal who ordered the Clone Army in the first place. We know it was Dooku, but it's never brought up. These are things that Lucas said would be answered in this movie. I hope it's explanied in the movie because the novel sure didn't explain it. It's also never explained how Palpatine managed to stay hidden for so long. Yes, Lucas has used the cheap explanation that the dark side is clouding the Jedi's perceptions but that's just pure rot to me. None of this is ever made any clearer.
In the novel, Luke is born first and Padme touches his head and names him. Then she drifts back into delirium and Leia is born. Padme never touches or holds Leia. So, in the context of the novel, Leia's feelings or images of her mother that she talks about in ROTJ don't make any sense. This might be different in the movie. I hope so.
The big thing that really bugged me in the continuity department was the duel between Obi-Wan and Anakin. During the duel, not once did Obi-Wan try and turn Anakin back to the good side. In fact, he didn't show anything other than the fact that he wanted to kill Anakin. Period. No remorse. No regret. Nothing. So the line that Vader says to Luke in ROTJ, 'Obi-Wan once thought as you do' now doesn't make sense. There isn't any indication that Obi-Wan went to Mustafar for any other reason than to kill Anakin. Padame on the other hand, she tries to turn Anakin back to the good side and even as she dies she thinks (and says) that there is still good in Anakin. Again, this might be different in the movie. I hope so.
Another point of contention for some might be the whole Anakin becoming Vader. It works on a certain level for me, but it feels rather weak. I had always pictured this as being a rather slow process. You know, Anakin starts using the dark side more and more and before he knew it, it had taken over. Sort of like becoming addicted to drugs or something. Well, this doesn't turn out to be the case. The transformation seems to be really quick and rushed. Anakin's motivations for choosing the dark side are rather weak. It boils down to his obsession to try and save Padme from death. There's more to it than that of course. Anakin's got Palpatine playing on his fears about Padame, his desire to have greater power and the fact that the Jedi appear to be using Anakin. Yes, the Jedi and Palpatine both put Anakin in a very awkward position. The Jedi don't trust Palpatine and want Anakin to spy on him and Palpatine doesn't trust the Jedi Council and he appoints Anakin to be his representative on the council to spy on them. So Anakin is stuck in the middle. He wants to be loyal to both sides, but of course that gets difficult when Palpatine tells Anakin that he's Darth Sidious. During the Mace/Palpatine duel, Anakin makes his choice. It's really not that he chooses the dark side, as much as he chooses the side that promisses him the ability to save Padme. It just struck me as weak. I have been telling my best friend for six years now that Anakin's mother and Padme were going to play a part in Anakin's destruction. While I was right, I just thought that there would be more to it than this. As I said, it does work for me on a certain level, but I was just expecting so much more. Knowing Lucas however, I shouldn't have. Deep or hidden meanings have never been Lucas's strong suit. Everything is pretty much on the surface. I guess I forgot that.
There are scenes in the movie that for one reason or another didn't get into the novel. The whole battle scenes on the Wookie planet (forget it. I'm not even going to attempt to spell it.). Chewbacca's rescue of Yoda isn't in there either. Now we know that we get to see the battle because it's in the trailers and it is talked about in the novel. However, Stover never actually takes us there. Lucas may not have wanted that shown in the novel and wanted for that to be revealed in the movie. I can't say, but it seems logical to me.
Some fans, myself included, are going to be really pissed off that other than one quick shot (and that is probably an interior shot at that), we never get to see Alderaan. I guess it doesn't matter that in twenty years it's going to be blown to bits. We aren't supposed to care. Bah! This is just poor writing on Lucas's part. A problem that could have easily been corrected if Padme had been from Alderaan instead of Naboo. Or Lucas could have solved the problem with just a few scenes on Alderaan in this movie. I'm not holding out any hope on this. Alas, poor Alderaan. We never really knew ya.
Overall, not a great novel. There was too much explanation of things that I really didn't give a damn about. I found myself bored several times by these useless tangents. Just tell me the damn story and keep the EU stuff for EU. An obvious lack of explanation (or in some cases no explanation at all) for events that I felt needed to have been explained better.
One final nitpick. The cover. No where on the cover does it say Episode III. The spine doesn't match the style that was used for both TPM and AOTC novels. If I didn't know that this was the novel for the final Star Wars film, it would look like every other EU book that is out there. Nothing to make it stand out as part of the movie series. Poor marketing in my opinion. Great artwork, though.