Thank you for the welcome. It's good being able to mix in with another side of the FS modding community.
I do like the idea of the multi-choice beginning. Of course, it would mean creating multiple campaigns or lots of missions that meet up at some stage for a single campaign. There's lots of possibilities to go around.
I can easily see multiple challenges for any reconstruction era fan. There's several to conquer and solve. All of them are pretty big, as I'm sure you can imagine.
The main one though is what are these factions really like? The names should give hints, but then again, they could be the opposite to what they sound like. EG. The Regulus Syndicate sounds like a roguish mob, but no way to be sure. This is where a lot of imagination is warranted. We do know that some time after the Great War, peaceful existence was restored and the factions eventually becoming merged into the GTVA, but not much else. (Just checking, the alliance was formed in 2345. Gah, I'll have to change the year in my mod.)
I think another main challenge is creating conflicts that have valid reasons or make sense. Apart from territory, I don't really see what they could fight for. But then again, there may be a many great reasons why they might clash with one another. Out of the four, I believe the Regulus Syndicate and the Adhara Coalition are the most likely to compete and have some sort of bloodstained history.
My reasons being, they are two systems apart and positioned on either ends of vital trading systems. You'd think things would be highly tense there, despite the fact that things should be relatively peaceful. I would think things would be in favour of the Adhara Coalition however. Namely for the systems they could control, unless the Syndicate controlled all the north-western systems, but unlikely if the Antares Federation ever wanted to invade Sirius and threaten Regulus itself. The Syndicate would probably only have Polaris as a sytem for keeps where as the Coalition would have Mirfak, Epsilon Pegasi and Procyon A.
Back to solving the challenges in my mod. "Scoots to the private laboratory"
Edit: Just out of curiosity, would it be viable for someone to develop a working prototype of the Prometheus-R cannon before GTVA engineers got to the idea after the formation in 2345? I find it hard to see how any Terran factions would be able to use the original Promtheus after the Great War. As stated in the FS2 Prometheus-R's tech descriptions, all supplies of Argon (needed to work the firing mechanisms of the cannon) were diminished. Unless a solution was made, everyone would be running around purely with Avengers and Banshees, unless they got hold of any secret GTI-tech of course.