Which areas are you refering to specifically? In your original 5 territories as Rome, IIRC you can't recruit native troops. In sicily you can recruit native troops and in southern italy. THe way it works is like this: The lower the government level, the closer the territory imitates homeland territory. A level 2 government can recruit a lot of factional troops; however since Rome has 4 levels of military reforms, the recruitment of the troops is limited. The higher levels of government (level 3 and 4) imitate more local types of government and allows the people in that territory more freedom, especailly culturally. You can build higher level's of regional Military Industrial Complexes (MIC's) as the level of government increases.