Hi -- in general, this is a great application of a great system to a fascinating set of strategic situations.
However, some of the mechanics related to civil wars seem to me a bit underdeveloped. I say this on the basis of a play-through of the Septimius Severus scenario.
It seems odd to me that area loyalties tend to be 100% toward one faction or another. Surely the provincial elites could not be so polarized between one contender or another.
Furthermore, it seems odd to me that most garrisons would fight so hard to defend a city against one or another feuding imperator. If there's a leader from the defending side in the city, than of course he would muster a defense. But if there were no such leader, it would make sense for the city to capitulate -- in most cases -- to acknowledge the claim of whichever army was outside its gate.
I don't know as much about the Roman civil wars as I do about other periods of military history, but I don't recall any episodes where a pretender would fight as hard to subdue an imperial province as he would fight to subdue, say, a Cantabrian or Gallic region.
Perhaps cities that don't have a leader or legion present would only close its gates to a civil war army if loyalty and national morale are high. This perhaps would add more to the political side of the game -- propaganda, subversion and the like.