So, with the Loyalist/Rebel splits in Rebellion, each faction obviously had reasons to split. TEC split due to differences to restore their empire- the Loyalists wishing to retain their remaining territories, and the Rebels using their fleet to reclaim their lost systems. The Advent split do to some sort of philisophical difference; the Loyalists being hardliners and the Rebels believing the Unity to have a far difference purpose. But the Vasari's reason seems a lot stranger. Why would this ancient civilization split into two group because of how they want to flee?
In the intro cutscene for Rebellion, the narrator mentions that the Vasari Rebels were outcasts of their own society. How could this happen? What it seems like is that the original Exodus Fleet, through the past thirty years of wars, has largely ceased to exist. This is not just because of predictable mounting casualties from the war, but due to the other remnants of the Empire. The Returning Armada signals remaining Vasari ships and gathers them to the Exodus fleet. Though this is in-game a force multiplier, it has a larger implication lore-wise.
I was looking at the Vasari Loyalist techs, and it led me to a conclusion. The Vasari Loyalists are not members of the Exodus Fleet. Once the Loyalists go full-mobile, they are summoning other Vasari remnants that predictably have the same ideals of the original Empire. As the mainline Vasari faction (From SOASE/Entrenchment/Diplomacy) had this ideal as well, the other remnants would likely have dreams of rebuilding the empire. The Loyalists are increasing their population entirely from the fleeing remnants, not from the Exodus Fleet. Their Titan is contacted from phase space, and it brings out more from phase space.
As the Vasari Loyalists are largely, if not entirely composed of "new" Vasari, they have far less personal experience with fighting the TEC and Advent than the Exodus fleet. Because they are entirely used to overwhelming victory, the conflicts with the now advanced enemy forces must be absolutely terrifying for them. This results in the Loyalists deciding to just pack up and flee the system, scared of both their unknown enemy, TEC, and Advent. They just want to jump out and continue their flight.
The Rebels, in contrast, are the Exodus Fleet. These are the guys who first entered Trader Space thirty years ago. They have been in constant contact with TEC and Advent forces for decades. As a result, I believe that they may have given up their "empire mentality", as it has proven to not work. The Exodus Fleet realizes that the Vasari are not invincible. Their only way to survive is to cooperate with their former enemies. Years of diplomatic efforts (As shown by Diplomacy) may have helped in forging cooperate behavior between the Exodus Fleet and thir enemies.
The new arrivals never had this type of experience, so the Exodus Vasari's ideas would seem preposterous, even blasphemous, to them. Rather ironically, the new arrivals cast the Exodus Fleet out of their new society, and began moving onwards. The Exodus Fleet, now known as the Rebel faction, takes their own path; to forge an alliance with their former enemies to ensure their survival. Though the Rebels also are contacting elements from phase space, it is far more limited than the Loyalists. This would allow the Rebels to re-educate the new arrivals about what is going on.
As I'm seeing it, this is the first true political split in Vasari history.