With the next update we have changed the way Rome is represented.
The current version of the mod has all of Rome's units from the various tome periods all in the one faction.
The new version will have them split into 4 different custom battle factions:
Rome - Camillian
Rome - Polybian
Rome - Marian
Rome - Augustan (The screen below has since been changed to Augustan)
Each custom battle faction will have the troops available during that period only.
This will help the AI pick proper armies in custom battles and add to the authenticity of the battle experience.