The entire Aggressive Negotiations conversation during the dinner scene between Anakin and Padme was ad-libbed by Hayden Christensen and Natalie Portman at George Lucas' request, due to his not being happy with the romantic dialogue he wrote for that scene.
Here's a creepy variant. When Anakin is about to go off and hunt down the raiders who kidnapped his mother, look at his silouette on the wall. Doesn't his head look... Familiar? And here's the thing: No one on the post-work team shopped that shot. Hayden/Anakin's shadow looked like that naturally. Possibly the only literal case of foreshadowing in film history.
The scene at Kamino had an interesting variation of this trope mixed in with What Could Have Been: When Obi-Wan heard of the clone army and the Jedi Army's supposed ties, the name of the benefactor was originally intended to be "Sido-Dyas", a thinly veiled alias for Darth Sidious, Obi-Wan was then supposed to state that he never heard of him, to which the Jedi Masters Mace Windu and Yoda will confirm that no Jedi Master existed by that name. However, the script writer made a typo in the name (replacing the "d" in "Sido" with an "f"). George Lucas ended up liking the typo far better than the original, so they rewrote the scene to reveal that Sifo-Dyas had died over ten years prior to the movie.
What Could Have Been: A deleted scene shows Anakin and Padme's sentencing before the arena scene. It reveals they aren't being killed for opposing the new Confederacy, they're being executed for murdering all those innocent workers and security in the factory before they can use their political clout to squirm out of responsibility.