Clone War, hands down.
To clarify–we are not talking about movies here. We are saying, regardless of how their story is told, which war (rebellion in the Imperial Era or civil war in the Republic era) is more interesting. Here is why.
Badass elite clones that learn to be individuals as they are spent for war is interesting. Nameless and faceless cannon fodder in blank white uniforms is less interesting. A purchased alien army led by jedi generals is interesting. A rag-tag collection of aliens whose only common ground is hate for the Empire is less interesting.
Droid armies with different units who have different functions, but overall act like an expendable multi-environmental customizable military is interesting. An army of clumsy cannon-fodder led by scowling Brits is less interesting. An army led by a Force user who puts aside the cherished moral codes of both Jedi and Sith, backed up by a cyborg, answering to a shadowy figure, is more interesting than a withered old man and Darth Friendly Fire.
Armies using smaller ships that can actually breach atmosphere and fight in formations is more interesting than vast ships with poor fields of fire. West End Games rehabilitated the Star Destroyers with much more utility than you see in the movies, but that’s not how they appear. And a handful of really massive ships seems less able to maintain galactic order than a larger number of smaller ships of the line.
Every side of the conflict has more interesting technology and equipment and vehicles in the Clone War. (Digression: even if the Empire decided to evolve those designs to be bigger and less effective, all that gear should not have disappeared overnight; the rebels [in the Rebellion and more garden variety local objectors] would be well equipped with the walkers, speeders, starships, and the like left over from a war that blazed on mere decades before.)
I do not like the prequels. But I do enjoy the Clone Wars animated show; it tempers the arrogance of the jedi some, and gives greater exposure to second and third tier characters. The show also walks the fine line of trying to make the primary characters the same and capture their essence from the movies, but also try to make them sympathetic.
A civil war feels different than a rebellion. An elusive and dark figure pulling strings to manipulate the galaxy into rendering itself unable to prevent him from taking over is very interesting. An elusive and dark figure sitting on the throne sending his lap dog jedi-killer and spies all through the galaxy is less interesting. The Clone War deals with how a hard-pressed government run by politicians struggles to keep its promises and protect its people during war. The Rebellion focuses on punching The Man and his servants in the crotch until they give up control of territory. (The Rebellion tries not to pay too much attention to how dangerous sudden freedom is to the liberated, until you get to extended universe material.)
Don’t get me wrong. The prequels angered me, and they degraded my ability to enjoy 4-6 because of how they portray events and characters who reappear in the later (original) movies. Even so, I have to admit… the Clone War is a lot more interesting than the Rebellion.