The final faction list is all the old factions minus House Renly (who has been removed from the campaign, and only is in custom battles), House Stark (who now is House Manderly) and House Tully (who now is House Frey).
So basically:
House Lannister.
House of Tommen.
House Greyjoy.
House Arryn.
House Martell.
House Tyrell.
House Frey.
House Manderly.
House Bolton.
House Stannis
And the rebels.