Episode III is definitely the best of the prequels, both visually and story-wise. I was very entertained. That being said, here it what bothered me:
5) R2-D2's Acrobatics - Most awesome, but it left we wondering why didn't he use any of those skills in IV, V, or VI. This one is forgiveable though, because of the height of the X-Wings compared to the ships in III and the fact that R2 has always done enough to save himself and others. Why show off if it isn't needed? Though Yoda and Obi Wan's age progression explains the reason they are less acrobatic, this one is less obvious.
4) Dialogue - I am lying a little here, because the dialogue didn't bother me that much. Some of the catch phrases stood out a little too much maybe, with the actors practically winking at the camera during the lines "I have a bad feeling about this!" but again, forgivable. The dialogue was fairly in league with the rest of the series.
3) Acting - Improved from Episode II. Still not great in many aspects, with the exceptions Tom mentioned above.
2) and 1) Blown Secrets - Okay, now for what really bothered me and the reason I am posting today. The last fifteen minutes of the movie blew at least two secrets from the original trilogy. Episode III seems to assume that everyone has seen IV, V, and VI. Of course, today, most people have. But future generations watching the films in numerical order are going to think that IV, V, and VI are lame because Episode III: Blew the secret that #2) Vader is the Father of Luke and #1) Luke and Leia are twin siblings. I think this would have been best left shrouded in mystery - We could have heard a baby crying and fans would know without having two of the bigger plot revelations screwed up.
Plus, couldn't at least one of the Jedi sense the twins? Maybe that is getting too personal?