The thing that most bothered me was the absence of my favorite Jedi character Shaak Ti, she's one of the main Jedi characters in the Clone Wars micro-series.
She was supposed to be one of the Jedi killed in the attack on the temple, Vader kills her while she's meditating, but they cut that scene from the movie.
However overall I thought the movie was one of the better in the series, definetly better than episodes 1 & 2