What just came to my mind is the question whether you want to build more of a Fallout-flavored-Civ4 or whether you are planning some deep Fallout-like mechanics, totally messing with the usual gameplay. Because if it's the latter case some ideas would come to my mind (although I'm not sure how well they would work out).
If I'm not mistaken than in Fallout 1 there where mostly singular factions which occupied mostly an area around their 'home' and otherwise maintained smaller outposts at best, like the BoS or Enclave. Of course, Raider- oder Slaver-like groups where everywhere but not necessarily as a united faction.
I wonder if it would be fun to play if a mod would replicate this kind of setting. I'm especially thinking of the Centaur-Race civs in the Master of Mana (or FFH-Mod in general), which have a capital city but get only outposts beyond that, i.e. cities of size 1 without cultural development. This sounds like a mechanic suitable to the BoS, for example.
Others, like the NCR or new Reno, might get only a capital and nothing beyond that. Of course, by taking away the expansion mechanic from civ, there would need to be some replacement so that it doesn't get boring to play.
(Also it's again a matter of the timeline scope. Over several decades I could see factions like the NCR spanning over multiple full-fledged cities, but if the timeline of the game would be limited to a shorter period the above description could even make sense.)
Another thing that seems resonable to me would be to have two lines of teching:
- A scavenging line for retrieving old techs or maybe some enhanced tech-stealing-from-others (the spy mechanics are a little clumsy in civ4 as they are right now).
- A research line in the traditional sense of civ4 which will give you high-tech stuff like energy weapons.
I must admit that I'm not sure atm whether the BoS researched its high-tech stuff itself or whether they only preserved it from before the war.
One way or the other, I would find it a bit odd if Raiders or Tribals would be the first to research power armor or plasma rifles before the BoS or Enclave could. But then again, giving those two too much of a head start would create a huge balancing problem.
Just some musings, I don't know what you're long-term intentions are for your mod

I will also try the newer version of it soon, I noticed that there was something new but was still in the middle of the current game and didn't want to drop it right in the middle.