The best way to go about this in my humble opinion is to have Rome as a single faction, but with powerful families competing to become Governors, Senators and Generals.
When you decide to create a legion you should be able to choose from a pool of noble families to lead it (on the list it'll show things such as command rating, loyalty and personal attributes) this kind of system was used in Napoleon total war to recruit Generals. Same thing goes for choosing the Governor of a province, should be able to select from a list of noblemen.
Among the most powerful families you have to do a balancing act, making sure not to make one family too powerful otherwise there will be dire consequences (civil war). The system only affects the recruitment of Generals, not how you use them. E.g you've recruited 5 Scipii Generals to lead armies but only one Julii, then tensions will rise.
I feel like there is more I can add to this, feel free to chip in with ideas along the same lines.





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