Many times these strange AI tendencies are part of our alternate history we create. Sometimes it's great that the AI is not bound to obey history. Other times, like when Rome ignores Epiros to go hunting rebels, it seems to be illogical and problematic. So maybe we need to focus on specific instances, such as the Romani and Epiros. I remember that vanilla RTW had no trouble making Roman factions go after their "assigned enemies", such as the Greeks, or Carthage. I think it was with a script? Maybe such a script would be useful here? It would be almost an act of insanity for Rome to ignore an invasion of the Italian Penninsula like this, so... maybe they just need a push in the right direction at the beginning of the game, just to keep them from literally completely ignoring a direct invasion?

And, I wonder, also, if bigger factions are percieved as a more serious threat, making the eleutheroi seem more threatening than they really are?