Despite people hating on him, Mauls Shadow Collective is the closest thing to a real third faction that the clone wars ever got (correct me if I'm wrong) despite the fact that it fell pretty quickly after Palps got involved (if I remember correctly).
The only other major faction that I can think of is the Hutts, and they were included in the Collective anyway. While the original release should probably just cover the republic and CIS, I reckon the Shadow collective is not a bad idea.