--- spoilers ahead ---
My main gripes with the film:
a) The first deciding fifteen minutes of the film, were full of silly practical jokes revolving around R2 and the oh so silly trade federation droid army. Not only did they go back to "Episode I - Style" battle droids - no, they let them talk much much more than they did in Episode I and what they talk is just plain, annoying silly. Having almost non-talking battledroids in AotC made the movie so much darker that it is really mind boggling to me how they could decide not to do that for RotS. Especially because the place where all this happens is supposed to be Grievous' command ship, the new 'cunning' cyborg commander of the battle droid armies. Well these first fifteen minutes will make you believe Jar-Jar Binks is now in command of the droid forces.
b) Grievous is a meaningless character that was merely needed as a plothook and then further abused by futile attempts to turn him into an uber-cool action oriented character. This character had much potential. He would have been awesome if the droid army would actually have been efficient under his command, but instead it is much less efficient than in Episode I. He would have been cool if he just had a shield generator and a combination of a laser-sword resistant melee weapon and blaster. Not using the lightsabers he collected (because of his deep hatred for the jedi) would have had him appear as a much much stronger character. Alas, all he really is, is a dull (and putting his overall inefficiency into account - rather unnecessary) replacement for Dooku (who had to be "killed off" to establish an important moment between Palpatine and Anakin).
c) Palpatine's makeup - at times it looks very good (almost still not as good as in RotJ) but at other times it looks really like he's overly fat. It's not very consistent. This would not have bothered on a side character - but failing to deliver a consistent look on palpatine is a goofup that distracts from the things happening at times.
d) You don't see wookies fight the way chewbacca did in the old movies, the only 'serious' fighting in a closeup scene is the scene I already saw in several teaser trailers. And that scene is ruined with another attempt at humor at an inadequate time - the return of the wookie tarzan call.
e) Violence dumbed down (you already can see this in the teaser trailer) when Anakin strikes down Nute Gunray, you merely see a superficial scratch like the sword had hit a metal wall, although anakins motion rather suggests slashing him in half. This method was first used in the Jedi Knight computer game series to reduce graphical violence and is rather inadequate at that point in the movie.
f) Vader's "Sith Eye" design merely resembles that of Darth Maul, which takes something away from the uniqueness of both characters Vader and Maul. I would have expected a deep pitch black in black for Vader.
g) Vader learning of the death of his love - too much b-movie drama, yet I expect to learn to love this because I love b-movies. I really had expected a direct confrontation between Vader and Sidious at that moment. Would have been a great way to establish the reason for Vader's fear of Palpatine.
What I really really liked:
a) How the core plot is handled by the main actors. Kudos to Hayden Christensen, Ewan McGregor, Natalie Portman, Samuel L. Jackson, Yoda (Frank Oz and Rob Coleman and his fantastic team of character modelers and animators) and last but not least Ian McDiarmid. These guys really deserve the main credit for me loving this film.
b) The final showdowns are some of the most intense ones in the entire prequel trilogy - not necessarily choreography-wise, it's hard to explain - the climactic nature really gets across because they really present a 'duel of the fates'. And yes the musical score may add a lot to that. *takes a deep bow before John Williams*. I agree with RRS that the Maul showdown remains the prequel fight with the best choreography.
Edit: I thought of it a bit and I think one of the reasons I like these showdowns so much is the places where they occur. Two former friends attempting to kill each other in the hellish environment of Mustafaar and two arch enemies fighting each other in a place that basically represents the heart of the galactic republic. Both very powerful images. Just overwhelming.
c) The execution of "order sixtysix" really got under my skin. I hadn't expected that to happen in that special way. Kudos to George Lucas, I liked that one a lot - really gave me the creeps to see such a thing happen in such a radical way.
Edit: What would really have been great and would have added a lot of importance to the wookies appearing in the film, would have been if the wookies would have played a major part in the protection of yoda from the execution of order sixtysix. Throwing troopers around growling and getting into an escape battle against the imperials to ensure yoda's escape from kashyyyk.
d) Cameo of Jett Lucas was awesome, usually I do not like that kind of stuff. A great last stand he fights there, he must have felt very honored to be allowed to do this scene.
e) The architecture of the Mustafaar base interior slightly resembling the area where Luke fought Vader on Bespin.
f) That it was unknown that there were twins and the fact that Vader kept the possible existence of a child secret from the emperor.
--- spoilers end ---
There were a lot more little things that I liked in this last prequel episode, it is really a good film. But because of the things I did not like as stated above, AotC probably remains the film that manages to convey a sense of threat and seriousness (with a few rare exceptions of course) that the other two did not manage to convey, although they had the potential to do so. What really stole RotS it's pole position among the prequels, is the time wasted on meaningless slapstick and purely decorative action sequences that could have been put to good use for the dramatic climactic scenes in the film that occasionally suffer from a lack of time to fully deliver their potential impact. At the moment AotC and RotS are head to head in my book.
All in all it is a very good prequel movie and you should all go watch it in a big theater, for I am sure you will enjoy it a lot (set aside from the disturbing things I mentioned). May the force (and the soundsystem of your theater) be with you. ^_^