I'm 3/4 of the way through - so I'll comment on a couple of your points...
1) I was surprised to find out that the space battle, duel with Dooku, confrontation with Grevious, rescue of Palpatine and crash of the ship took up 100+ pages in the book. I thought all of that stuff was supposed to take place in like 20 minutes of the movie! If the movie is two hours long, why does a segment that is only 1/6th of the movie taking up 1/4 of the book?
So my point here is that I think the author decided to focus on the core dynamic of the movie. It's great eye candy that Yoda goes to Kashyyk and first helps the Wookies repell the CIS invasion force and then the Wookies help him escape his clones when they go Order 66 on him. So again, the author may have chosen to focus on Anakin, Obi-Wan, Palpatine and Mace instead and decided to expand on events surrounding those characters instead of scenes that are in ROTS for fan-boy placation and ILM to pound their chest proclaiming "Look What We Can Do!" - just a thought...and this goes on further to #2....
2) I think the deaths of other Jedi around the galaxy at the hands of their clone charges will be handled quickly in the movie as well - we really only need brief establishing shots and then see the clones fire on the Jedi. This is something I can see a book glossing over easily (and remember I haven't gotten there in the book yet) since the book can have some narrative explaining that the extinguishing of Jedi around the galaxy is felt by Yoda - in a movie you can't really express what a character is feeling except through dialogue or action - so the best substitution would be to show quick scenes of Jedi dying.
3) You are right, I too was surprised at how much of a "jerk" Mace Windu is portrayed as. The book gives you insight into the mind of Anakin and Obi-Wan, perhaps the portrayal of Mace is further enhanced by how Anakin feels about the way Mace is acting towards him or the secrets Mace is forcing Obi-Wan to keep. In reading the book you definitely feel like Mace is squeezing both Anakin and Obi-Wan REALLY hard and is almost the true reason why everything transpires as it does. However the book also is clear to bring up a couple of other points:
a) The dark side is making things incredibly difficult for the Jedi, even going as far as tainting some of the Jedi through confusion - the Dark Side is definitely working against Mace and he is definitely fighting on a daily basis from giving into the fear of losing control
b) Palaptine, several times, reminds Anakin that those who have power are always afraid to loose it. So I think the book is trying to show that what Palpatine is saying is on one hand subterfuge of the Sith, but on the other hand there is a kernal of truth. Just like when Dooku tried to convince Obi-Wan to join him to bring down the Sith in AOTC. Dooku's mojo didn't work on Obi-Wan, but Palpatine's is DEFINITELY working on Anakin.
My BIGGEST disappointment, and again I haven't finished so it still a possibility, was that we didn't learn that the death of Shmi was orchestrated by the Sith.
I would have thought that in ROTS we learned that Sidious (who the book says HAS been working grooming Anakin as his next apprentice, which we already knew) had Dooku arrange for the Tusken Raiders to kidnap and torture his mother. A tactic that Darth Vader uses in ESB when he tortures Han, Leia and Chewie to draw out Luke. It would definitely be an interesting connection between trilogies to see that a common tool of the Sith when trying to trap or turn a Jedi is to torture those the Jedi cares about. An excellent place for this to come up is in the beginning. Obviously through the shadow of the Dark Side, Sidious talks to Dooku right before he starts to fight Anakin and Obi-Wan, through Palpatine. It would have been easy to have Sidious instruct Dooku to tell Anakin that he was behind the death of his mother. This would have fueled Anakin's rage towards Dooku and he would have even more easily given in to his anger when he faced Dooku - which in turn would have furthered his advance towards the dark side.