I'm sure this is already decided, but I would just like to throw out a few thoughts on the coming r/evolution of factions.
tl;dr: The Sczarni and Cheliax factions are evil and self-serving entities that violate the fundamental team basis of the campaign, and should be removed as legal player options.
(Expecting a bunch of flames from members of those factions, of course. All I ask is that you read my arguments and think about them from a campaign perspective before writing.)
Let me first declare my allegiance to the Society above any political allegiance (even the Grand Lodge, which is after all dedicated to a political organization - the Decemvirate). I lobbied for the minimization of faction missions as soon as I realized Paizo actually listened to its audience. So overall, I have been very happy with the turn of events so far. But, over the past year I have had several issues related to factions, despite their less-dominant role in the rewards earned by characters. These issues revolve around two specific factions which will surprise very few:
On the Sczarni: Why are they a legal player choice when an evil alignment is not? The Sczarni faction are a group of people who basically are telling us, "I'm just here to make money, screw you guys." This is the textbook definition of a neutral evil outlook. I understand why they want to be in the Society, and even why (in-game) the Society allows them in (because of their vast intelligence network). I fail to see why they are a legal player option, though, given the group nature of the PFS play experience. They were accomplices in the biggest betrayal of the Society we've seen in five season of play. Their older faction missions are about stealing from the Society, extorting people while on duty as a Pathfinder, and lying and cheating their Society comrades at the table. Now, many factions have secrets, and many occasionally ask their agents to do questionable things, but the Sczarni routinely top the list in terms of "un-Pathfinder-like behaviour".
On the Paracountess and Cheliax: First, fanboi out of the way: one of my favorite NPC's ever! BUT - her stated goals for Season Five should get her executed for crimes against Golarion, and any agents that actually help her advance them should be thrown in irons as traitors to the Crusade and the Society. I don't really see how any non-evil PC can willingly be a member of her faction anymore. (I know John and Mike must see this, too, so I can't wait to find out what they've got in store for us... )
While both of these are great in-game story lines, I suggest that by their nature the Cheliax and Sczarni factions pose a major problem for Organized Play. As PFS grows and new players join without knowing the setting or the campaign background, they see these legal player options and are totally misled about the nature of the campaign. The Guide tells us "..when you find yourself doing everything in your power (...) to undo everything [another] character is trying to accomplish, you’ve probably lost sight of the purpose of Pathfinder Society Organized Play". Both the Sczarni and the Cheliax faction missions in past years, as well as the Paracountess' goals for Season Five, do exactly this, and tell their followers to do it, too.
This is not just theoretical: Of the four new-ish players I've had to talk to about alignment, PvP, and team-play recently, both FtF and online, three have been Sczarni and one has been a Cheliax faction member. I've had Sczarni players argue that since "no PvP" specifically defines itself as "don't kill another PC", that it is legal for them to intimidate, punch, or knock out other PCs, so they can do some Sczarni stuff without being caught. I've had Sczarni (and one Chelaxian) argue about the exact line where things become "evil", and use faction goals as evidence about what "must be legal" since it's a faction goal. I've had members of both factions withhold healing from anyone who disagrees with their Neutral Evil-style actions. I've had to invoke "don't be a jerk" several times on these characters.
I contend that, no matter how much "fun" they are to the members of these two factions, the in-game goals and outlooks of the Cheliax and Sczarni factions are at odds with the stated campaign goals of no evil PCs and no player-versus-player combat. We are setting up new players to run afoul of the campaign rules by giving them in-game permission to be evil (usually spelled "chaotic neutral" on the character sheet). To work in the PFS OP campaign, both factions need to be completely revamped or removed.
I hope that some of these issue can be resolved before Season Six. I'd love to find a way for both factions to become more in keeping with a group-based game, but given the Paracountess' recent actions I can't see any way for her to live except as a fugitive.
I'd love for someone to change my mind with additional evidence or show me what I'm missing in my thought process here!