Well, some other thoughts about possible factions (I´ve come up with some basic rules for a Great War campaign a long time ago, sadly we could never play it here in my group):
I´d specify three different factions: Vorlons, Shadow, and the Army of light. Every player would have to decide on one faction at the beginning of the campaign, with the opportunity to change allegiance once (has happened quite a few times in B5 history). The fleet-layout should be something like this:
Army of light:
- League
- Minbari
- EA (Sheridan: 3rd age or early years (representing the rag-tag rebel fleet))
- Narn
- White Star fleet (replacing the ISA; White Stars and Nolo´Tars only)
- Centauri (House Jaddo + associates?)
Every member of the Army of light would be able to take up to 1 fleet point worth of White Stars as allies (Nolo´Tars reserved for the WS fleet)
Agents of Chaos:
- Shadows
- Drakh
- EA (Clark) (3rd age, + Shadow Omegas obviously)
- Black Ops (still talking about 2nd ed. here

)
- Drazi/Brakiri (Vree-fluff in SFOS says that they abhore the chaos of the shadows; Abbai and pak´ma´ra are to peaceful)
- Centauri
Drazi and Brakiri pure fleets only, no cooperation/combination. Drakh as possible Allies for agents of chaos?
Agents of Order:
- Vorlons
- Minbari
- Abbai/Vree (paks too?)
- Narn (followers of G´Lan)
Maybe Agents of Order/Chaos could get the ability to "call in" a few Vorlons/Shadows in their games. Army of light would be able to to the same with the First Ones.
For example: every faction within a given campaign group would be able to use 1 First One/Shadow cruiser/Vorlon battle group in a single game within the campaign, if they decide on it before the game (putting it down secretly on a piece of paper or such). That would most likely be a matchwinner for one game.
However, following the B5 timeline, the campaign would most likely be decided in a final confrontation at the end, so it wouldn´t be unwise to keep that little extra help for the deciding battle.
OR: When coordinated centrally, each side could have a certain amount of times they would be able to call Ancient support over the course of the campaign.
I´m not sure about the Dilgar - obviously, they should be allowed to take part in the campaign, even if they were technically already extinct at that time - I´d say they could choose between Army of Light or Agents of Chaos.
Raiders would be able to choose freely. Did I forget anyone?