Q. Which things that are currently hardcoded do you plan on changing (e.g. number of men per unit, faction limit, number of factions that are controlled by the Senate?)

A.None. The way factions are managed is more flexible now, but that's something that most people won't notice. Actually, the Senate is gone in BI; by the late 300s they were no longer a significant force in Roman politics, so they won't be 'controlling' anyone
Ok I know very little about programming but something tells me hardcoding factions numbers is probably one of the easiest things to change.