I know it would need a complete refit. There are many things that don't fit at all but I'm considering making a version of the game during Clone Wars.

The overall objective of both sides would be the same. The Separatists will win when they gain enough support, and the Republic wins when they defeat the "Separatist Leaders" (which would be the equivalent of the rebel base)

Then there is the problem of the Death Stars, which I think should be removed altogether.

The characters would all have to be different. If we take 12 characters for each side, we will have:

REPUBLIC

Bail Organa

Palpatine?

Yoda

Obi Wan

Anakin

Padme

Rex

Cody

Tarkin

Yularen

Ahsoka

Mace Windu

SEPARATISTS

Darth Sidius?

Dooku

Nute Gunray

Asajj Ventress

Grievous

Durge

Cad Bane

Admiral Trench

Poggle the Lesser

Wat Tambor

T-series tactical droid

Moralo Eval

And lastly all the ships would also have to be different. Even if Republic=Empire and Separatists=Rebellion I think the ships and units should be somewhat inverted. Although there is a problem with the Shields/Ion Cannon, because both sides should have walkers (ATTEs and Spider Droids)

REPUBLIC

Venator class Star Destroyer = Mon Calmari

Arquitens Cruiser = Corellian Corvette

Consular Frigate=Medium Transport

ARC-170=X-Wing

Y-Wing=Y-Wing

LAAT=SnowSpeeder

SEPARATISTS

SSD = Lucrehulk

Star Destroyer = Providence Destroyer

Gozaniti = Munificent Frigate

TIE Fighter = Droid Starfighter

And of course, Battledroids and Clone Troopers as the each side's troopers.

So, there are lots of problems with all of this, changing things or removing things might kill the delicate balance of the game. What do you think? Any ideas?

Replace Palpatine, maybe with a jedi like Kit Fisto or something.

I think you could maybe have a cool system where every few turns Palpatine will join the leader pool of one side or the other (depending on some trigger, maybe a dice roll). Palpatine then could activate a system, causing all enemy units of Palpatine's controller's choice to head to that system, then resolve a combat if necessary.

Players could also attempt to capture Palpatine to prevent his wildcard sort of play from interfering with their strategies, with Grievous and Windu getting bonuses for these missions.

That could be a neat way of showing how Palpatine really pulled the strings on both sides.

This is really cool.

the only way you could accurately represent the Clone Wars is as a 3 sided affair. Where Darth Sideous is his own side that tries to manipulate both sides into prolonging the war. Whereas both sides are trying to win a quick victory Sideous is trying to weaken both sides so much that he can take control of whoever the winner is.

So in short. You would have to foundationally change the nature of the game. Really you'd have to make a new game. Which is fine. But using the Star Wars Rebellion mechanics you really couldn't make a Clone Wars version with a mere expansion. You could use some of the same mechanics like construction, leaders and fleet movement in the Clone Wars version. But probe droids, objectives, and the general asymmetry of the game would have to be thrown out.

The clone wars were far less asymmetric than the Galactic Civil War.

Yeah, I'd agree that the "cat and mouse" aspect of the Galactic Civil War is a little less applicable than that of the Clone Wars. I guess the Separatist Base could replace the Rebel Base, but if the Republic's job is to find that base and if the combat is less assymetric, then I think the CIS needs a different victory condition than "wait out the game". Perhaps they need to kill a certain amount of Jedi, or take over a secret configuration of planets (for instance, draw 10 random cards from the probe deck- CIS wins when each planet has CIS loyalty).

Personally, though, I think the Clone Wars work much better in a game like Risk than this. To be honest, same goes for the new trilogy stuff, at least what we've seen so far. It doesn't seem like the First Order or the New Republic/Resistance are significantly larger than one or the other. In fact, it seems like both lay kind of adrift in the ashes of the Empire.