Love them or hate them there are some very epic battles fought in the Clone Wars, and the TV show really fleshed out that era with some quality stories and amazing set pieces. I personally would love to see a separate prequel game called the Clone Wars built on a similar fashion.
Seemingly Equal-ish footings to begin with forces-wise but Republic has much higher production values and Separatists have weaker units, so quickly the Separatists will be outmatched and on the defensive. Separatists have the outer rim and Republic has the core.
The Separatists have a secret base that the Republic must find to eliminate the Separatist command and thus find out the identity of Darth Sideous and foil his plot. They can capture Separatist Leaders and if they get them back to coruscant the Jedi decrease support for the Separatists (decreasing the "reputation" track which could be called chaos track instead)
The Separatists must strike out and kill Jedi leaders, complete secret missions and sow a certain level of destruction (similar to Rebel objective cards) to increase the chaos track and decrease the rounds in the game thus paving the way for Order 66.
You could still have the time limit by having Order 66 which would end the game in favor of Darth Sideous (The Separatists).
Heroes like:
Republic
Starting: Obi, Anakin, Mace Windu, Yoda
Additional: Ahsoka, Kit Fisto, Plo Koon, Agen Kolor, Aayla Secura, Quinlan Vos, Ki-Adi Mundi, Sassee Tinn
Separatist
Starting: Dooku, Grievous, Asajj Ventress, Cad Bane
Additonal: Wat Tambor, Nute Gunray, San Hill, Poggle, Tikkes, Po Nudo, Admiral Trench
Units:
Republic:
Venator Class Star Destroyer, Republic Assault Ship, V-Wing Fighter, ARC-170 Clone Turbotank/AT-TE, AT-PT, Clone Trooper
Separatist:
Invisible Hand, Droid Control Ship, Vulture Droid, Destroyer Droid, Battle Droid
And as a twist the Separatists could have the super weapon Malevolence Ship which can be used to stun enemy ships during the first round of combat, but the Republic could deploy Jedi Knights to place sabotage markers on Separatist production.
Could even be a rogue element like Maul and Savage Opress that control "neutral worlds" and have to be defeated to gain support one way or the other.
Anyways I'm a massive fan of Rebellion and think that a Clone Wars game would be an amazing next direction. Definitely better than doing a First Order versus Resistance one.