Under the current system there is no way to represent factions interactions with certain regions like Rome's alliance with Syracuse etc.
That's what the Lvl 4 MIC represents, no? Here's a list to explain:

Level 1: Homeland- Field Native Troops, Pay Taxes, Culturally Identical, governed by your faction
Level 2: Province- Field Most Native Troops, Pay Taxes, Culturally Similar, governed by your faction
Level 3: Subjugated Land- Field Most Local Troops, Pay Some Taxes, Culturally Different, governed by puppet rulers or rulers subject to your government
Level 4: Allied State- Field Local Troops, No taxes, Culturally Independant, totally self-governed

Syracuse was basically a Lvl 4 province of Rome, in game terms.