In Episode II, a few background speeders were removed from the chase sequence (I guess so we wouldn't forget to focus on the characters; you know, because the audience is essentially a dumb animal with the attention span of... hey, I found a nickel!) and Anakin's breakdown in the garage is extended (MORE HAYDEN! YAY!).
In Episode III, one of the wipes is changed to a normal cut and... that's it. No, I'm serious, that's all they changed. Why they even bothered is beyond me.