Like most expansions,
Clone Campaigns adds a few new units to the fray and fixes a few of the imbalances in the original. The most notable changes are the two new factions, The Republic and Confederacy. Since the campaigns tell one arching story, you must play them in order. The first seven missions involve a Chiss Jedi named Sev'Rance Tann - Count Dooku's apprentice, while the last six involve Echuu-Shin Jon (players will remember him from the Rebellion campaigns). At first, I wasn't too jazzed about having to do this, but once I realized how deep the story went, it was really cool. Rather than retell parts of the movie, the expansion fills in a few of the gaps and works around the movie. While the game sets itself up for a 'good guy - bad guy' scenario, as the plot thickens it becomes harder and harder to tell who the 'good guys' really are. After completing the main scenarios, a special campaign is unlocked which involves the aftermath of Return of the Jedi and a very cool unit.
While both factions share a number of similarities with the original six, there are enough differences to make them worth using. For example, the Republic gets quicker, cheaper air and mech units as well as the added advantage of the Jedi starfighter, which combines the effectiveness of a starfighter and gives it the capabilities of a Jedi. On the other hand, Confederacy worker units are stronger and better able to defend themselves. In addition, their animal nurseries have the ability to producing predator units. These cheap, effective units are an added boon to the Confederacy and I can definitely see some strategies popping up around these units.
Two of the biggest changes to the overall game are, at first glance, rather trivial. The first is the power droid. These are perhaps the most useful units in the game - especially for players like myself who set up satellite bases all over the map. This is essentially a mobile power generator and while I wouldn't recommend them as a substitute for the real thing, they go a long way in supplementing them. Jedi have also been made more effective. Masters can now regenerate hit points (an ability that was until now given to certain Jedi) and are cheaper to produce - making it possible to send a sizable group of Jedi into battle with your armies.
In order to help balance out the factions, each of the original factions now have brand new units. The A-wing starfighter is now a part of the Rebellion's already formidable fleet and AT-ATs can now receive an upgrade that allows them to shoot at air units. Although mostly a cosmetic change, Naboo mounted units now ride sabercats. All factions also gain use of the Air Cruiser - a very powerful, and expensive, unit that becomes available later in the game. While slow and vulnerable, this unit makes up for it with its amazing range (more than even the best turrets) and firepower.
I could go on about the balancing issues that have been fixed, but then I'd probably just be rewriting the manual. It's obvious that someone was listening to fans since just about all the fixable complaints have been dealt with.
For the creative, Clone Campaigns offers a very good scenario editor and while the layout is hard to use, it's still cool.