The segment where the player fights Grievous' magna-guards in the command bridge of the ship while it has turned upside down was to be incorporated into the film, but it was scrapped and the concept was instead used for the game.
Likewise, another segment where the player fights through the fuel tanks of the ships was also intended to be part of the film, but was also scrapped and used for the game. This was alluded to in a deleted scene in the movie where Grievous corners Obi-Wan and Anakin and kills a fellow Jedi being held hostage; afterwards they use their sabers to cut a hole in the floor and drop down. That scene was to be the intro into the fuel tanks.
The game contains a bonus mission that lets you control Anakin during the epic duel with Obi-Wan Kenobi. If you manage to beat him, you are treated to a cutscene of Anakin betraying Palpatine and becoming the Emperor!
The game features many things that were cut from the movie, such as Clone Assassins.