To change who owns a city, cut the entire entry for that city (starting with "settlement") from its current owner and paste it into your faction's settlement list. The hardest part is not adding the city, but moving out the previous owner's units! I don't know what happens if you leave them there...
To PREVENT the Marian Reforms from happening when you make cities larger, make your faction the ONLY ONE able to build the imperial palace. After you build it yourself, you can re-edit the file to let others build it too. That way, you decide when the Reforms happen, and if you want, you can stay at level 4 for a good long while and really get to know your trarii.
Bookmarks