From a gaming perspective, the Clone Wars stands as one of the richest time periods to set a campaign. The reasons are many:

It's a freer time frame in Star Wars continuity. In the Rebellion Era, character choices are too limited, in accordance to official canon - no Jedi, because there remains only Luke, Obi-Wan and Yoda; no alien species, because they are enslaved by the Empire, and suffer from racial bias; no other villains but Vader and Palpatine, and those two live at least until the explosion of the Second Death Star... In the Rise of the Empire era, there's much more freedom to play - if all gamers want to play Jedi characters, they can; if all gamers want to play with different alien species, they can; if gamers want to side with the Separatists (allied with the Sith!) or with the Republic (secretly and unknowingly allied with the Sith!), they can. Besides, the upcoming motion picture (come August 15th!) and the TV series can be good sources of inspiration for upcoming storylines.

The Clone Wars are a more nuanced time frame, full of "gray areas". There are no clear heroes or villains. In the Clone Wars, "There are heroes on both sides. Evil is everywhere" (Episode III opening crawl). The point is even clearer in the scene where Padmé pleads Anakin to call on the Chancellor to resume peace talks with the Separatists. Her words are: "This war represents a failure to listen. Now you're closer to the Chancellor than anyone. Please, ask him to stop the fighting and let diplomacy resume." This call for sanity, however, was very late to alter the course of events - events that were carefully orchestrated by the Supreme Chancellor to acquire "power, unlimited power".

In gaming terms, this means that they can start siding with the Republic, and then change their minds as the campaign advances; or, sometimes, the opposite can occur. Anyway, it's a more open approach to roleplaying than the "Light x Darkness" feel of the Original Trilogy.

The Clone Wars are also a great time for huge feats of heroism. In the Original Trilogy, the most important victory to be achieved was already done by a party of heroes, and there's nothing that can be done to alter that fact. I wouldn't, as a Gamemaster, send players to destroy the Death Star unless their characters were named Luke, Leia, Han, Chewbacca and Obi-Wan. This would be sorely predictable, and not a very enjoyable roleplaying experience, as far as I believe. During the Clone Wars, players can destroy mega-weapons, yes, but they can also rescue helpless Systems from the clutch of the Separatists, aid in the war efforts, among other adventure ideas. There's a three year period (22 BBY to 19 BBY) in which many tales can be told, and are already being told in movies and books and comic books.

So as to avoid the commonplace "go to distant Planet, fight bunch of droids, save the day, return to Coruscant", there are many "special missions" on development. Field battles, Senate intrigues and plots and special missions will all be equal parts of the campaign. Stealing plans for a powerful Separatist weapon, preserving valuable Systems under Republic control, rescuing important figures in the War, those are some exemples of the special missions the characters will face. This will all be done over the backdrop of a massive conspiracy, that runs under the politicking of the Galactic Senate, and may spell doom to the Republic...

It's important to remember that the Clone Wars are being fought in two fronts -- with arms and words. The Republic won the war but lost its freedom: "So this is how liberty dies - with thunderous applause", sighed Padmé Amidala in the Senate, shortly before her death. Better yet: did the Republic win, or did it lose the ultimate battle due to Palpatine's treachery? How did the situation get to that point? How could the characters prevent - or influence - the final outcome?

Those are important questions to consider while planning a campaign set in the Clone Wars timeline.