Even though the Roman Civil War is out of EB due to practice and principle I believe they, if implemented, would add a lot of challenge to the Romani player. Often by the Marian Reform you can field tons of armies and have probably conquered half of the known world in the process, so the presence of a big hostile force inside your own borders should increase the Roman challenge well within the boundaries of historicity.

The rationale is: given the fact that the commander of a legion often paid for it, not the state, the Marian legionaries had their loyalty shift gradually from the Republic to their paymasters, usually a wealthy man with enough influence and good lobby among settled veterans and the major political factions.

I was thinking that instead of the hassle of adding "Roman rebels" as a faction, there could be instead a scripted spawn of random and big eleutheroi stacks to the SPQR faction, representing a potentially rebellious commander. It should be decided based on the loyalty and other traits of your generals, as well as other factors, some completely random; what exactly they could be, I'm still thinking of.

So we get those big eleutheroi legions, often commanded by family members, and then as the Roman player we must decide on what action to take, often taking their extermination as top priority. Rebellion, after all, can be worse than external wars.

The Augustan Reforms could be tied to rebellions, too, since overthrowing the Republic would be far bloody and would collide with many interests.