Well, I'd like to throw the Sith Inquisitor and the Jedi Consular in there. Both have their own (rather different) armies and supporters.
Also, Queen Talia of Onderon and Queen Amidala of Naboo might be interesting.
-The Infernal One/Sao, with his powerbase from the Operation (Maybe we could put him against Kephess and his army from the Operation)
-Lord Hoth and his Army of Light
-Empress Teta and her Armies and Fleets
-Cole Centarus leading CorSec
-Mentor + Directive 7 droids
-The Exile with all her Forces from the Battle against Nihilus (Telos Security, Republic Fleet, Companions, Mandalorian strike force)
Also, as comic relief: Sandpeople vs. Jawas (with droids)
I also got the idea to simply use several Flashpoints (for example, Darth Ikorel and his forces, Prophet of Vodal and his forces, Hammer Station etc.). But maybe I should start my own flashpoint vs. flashpoint series for this instead.
Those are some great ideas. A flashpoint vs flashpoint series would be neat.