Fight on either the Light Side or Dark Side. The missions are essentially the same, except with a simple character swap. The one except is the Mon Calamari mission in which the end boss is radically different.
Star Wars: Planetary Forces @ Toonami: Lost Data

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The hardest level is the Kit Fisto Mon Calamari mission. That's only because the boss is fairly random, unless it falls into a jumping pattern. Then it can be destroyed with ease.
Now, if only Timothy Zahn's Heir to the Empire trilogy were made into a cartoon, the world would be perfect...