In Pathfinder Society, everyone works for someone else. Even the "basic" faction (The Grand Lodge) effectively gives you the same advantages as people who work for someone. The vanities presented in the Field Guide are a nice touch, but they don't really make the faction come alive.
In Living Greyhawk many meta-orgs were run by player-volunteers or by the triads and were either very involved in adventures or very little, depending on the region (and they had nothing to do in the Core adventures).
In Legacies, you have a choice of joining - or not - one of the patrons. Patrons may sometimes ask things of you that are not in the best interest of the adventure, sometimes they will. Whatever the case, picking a patron is a non-trivial choice.
Although the patrons leaders are given an alignment, I strongly advise AGAINST choosing a patron on the sole basis of alignment "I'm lawful good so I have to work for the Sheik" is a very BAD way to pick a patron. These patrons act based on their goals first and foremost.
One word I've been chiming everywhere is "Choices" one of the things I think PFS is missing, a notion of non-trivial choices. This is a HUGE difference in philosophy. NeoExodus Legacies trusts and empowers its GMs to make the adventure fun, stick to the script as close as possible, but to change the adventure if the PCs are having too easy/hard a time with it.
One of the things I have not really seen much of in in many other organized play campaigns other than the Arcanis campaigns is "sideways" discussions. I mean having player-on-player interaction where the players have to discuss and talk among themselves what they want to do, how to do it and IF they want to do it. It is one of the staples of home games and one of the biggest thing lacking in Organized Play. If you ever played with me, changes are I spend more time, as a player, talking to other PCs than to the GM.
The trick - and hard part of that - is in the writing and presenting.
Why are they that way?
First we want to have factions similar to what Pathfinder Society had: nation-based plus the Sanguine Covenant. However that was a little too inflexible. People in these nations have a story, influence events and oftentimes have their own agendas that are not always in-line with their nation.
For example, in A4-Slavers of the Dominion, the PCs are hired by Grofka Polina to perform a task that could make things worse for the Protectorate. Better for her - and people in general - but could put the Protectorate in some diplomatic trouble.
I wanted the patrons to have the freedom to evolve and change based on the actions of the PCs and as the storyline evolved. So we needed a way to make patrons related to, but have some measure of independence towards their home nation. Finally, the idea was to have patrons be a subgroup of the nation. The faction would work for a leader who's interests were tied to one of the nations.
Surprisingly, this added a lot of freedom. Now, a PC would not work for the Arman Protectorate, but they would work for Grofka Polina. They would not work for the Caneus Empire, they worked for Lady Elsae.
The freedom from this, as a writer and a storyline guy was that these patrons could form enemies, and these enemies could come after the patrons' agents (the PCs). Same thing goes for allies. Now the PCs are immediately involved in a web of intrigue.
I believe it makes us very resilient and responsive to events. And though I really should not tell, the Patrons will often take an active role in missions by hiring adventurers.
Although we have no plans for this to happen, a patron could be ousted/ replaced. New ones could be added (we debated having "Section Omega" and the "Order of Kaga"...). In the end, Section Omega was not chosen because of its very tight focus on psionics while the Order of Kaga felt a little too much like PFS in its focus. In short, we reserve the right to play nasty tricks on them.
What does a patron give me?
A patron provides you with a measure of protection from other factions in the world. They may provide you with additional information about the adventure. Some adventures may provide you with unique opportunities and information.
Patrons are a way for you to immerse your character in the politics of NeoExodus and gain instant allies in the setting. You are gonna need all the friend you can get.