All,
  OK, so I am setting up some factions for a small corner of Near.
  I created a little place called Sanctum. Its a new Marldor castle town with an old Maldor city nearby. Its on the border of Ammeni (also, near the back woods of the old Zaru nation).
  The idea is to have stuff happening so that the place feels alive when the game starts (this is how I prep for a game, I learn the rules and then setup factions so I can make NPCs on the fly). Then chargen and I adapt to what the players want/need.

So, here is a google spreadsheet with the faction info I have so far:
http://spreadsheets.google.com/ccc?key=pJsDLey3h-2mj8SZibHu2Vw

Lemme know if anything doesn't make sense or if you have anything cool to add to it.

That's a rather comprehensive preparation, I like it. Perhaps building it into a non-linear representation, such as an adventure map or several, might make it easier to use?

Did you create the factions by taking the three cultures and the issue of reform as binary political leanings and then going through all variations? Interesting approach, that. You seem to be lacking one faction, somebody who supports the existing order but resists all three cultural spheres. Perhaps there just isn't anybody like that in the city.

Do you have any further material on the different factions and NPCs, or are you going to improvise as necessary when the game happens?

Eero,
  The process was like this:
1) Read up on Zaru, Maldor and Ammeni (cuz I was fascinated with the Zaru magic, but didn't want to make a campaign based on slavery as the centerpiece).
2) Came up with a setting that seemed like a good centerpiece for conflict. I came up with Sanctum, a struggling Maldor city on the Ammeni border and within spitting distance of the old Zaru territory.
3) Populated it with interested parties. I wanted at least two factions for each major factor (Maldor, Zaru, Ammeni, Merchants). But I kept going with what seemed to fit. Then came up with a faction leader and a starting contact for each faction.
4) Thought about what issues would divide them (reconstruction/reform, etc). And prioritized them from most divisive to least divisive.
5) Good catch, I did assign each political issue binary values. I used the binary values to determine who were real enemies and allies. The idea was to break free of stereotypes and find factions that had real issues that probably could not be overcome.
  The math stuff is not necessary, but it helps force me to think outside of the box. Its tricky though, I have to get a lot of the creative stuff out of my head before I start the maths, or the following material ends up much less creative and more methodical.
  Yeah, I don't like to go too much deeper than this until the characters are made and I have a lens to come back and view this all through.
  Does that answer your questions?

Yeah, that answers me. Your thought process about wanting to play with Zaru but wanting to avoid making slavery a centerpiece resonates with what I've been thinking about lately in relation to campaign frameworks - didn't I write to you about how Zaru and slavery are a very common campaign framework? It'll be interesting to see how Zaru shape up outside their slavery context.

Eero,
  Yes you did.
  Actually, that was my thought process as soon as I read the Zaru write up.
  I understand how slavery is a big issue and it is certainly a core problem with that culture. But I don't think that can be addressed properly without blotting out every other setting element.
  To me, the pacifism is a much larger issue tht can more interestingly addressed with this setting. In fact, that is probably why they are slaves, no? I mean with the power of Zu, they could forge their own destiny, but the language itself, reinforced by the culture, has subjegated them more than the Ammeni, I mean Khale has been able to resist them...

All,
  This is what I had in mind when I made this:
http://tsoy.crngames.com/Dave%27s_Life_Path_System
  I need to come back to it and see if I can tweak it to match this sub-setting better.
  Does anyone have any ideas?

Hi!
  I realize that the spreadsheet I made is not very helpful if you can't decode it.
  So, here is the decoded version.
  Some of the information is still sort of in my own lingo, so please feel free to ask if you have any questions.

Factions:
Trade Guild
An independent organization trying to make international trade easier
Ruler: Berny
Reform: Pro reform. Believes the old ways never worked
Maldor: Anti-Maldor. The empire is rebuilding, this is a bad thing
Ammeni: Anti-Ammenite, Ammenites are wicked and have no place in local politics anyways
Zaru: Anti-Zaru. Zaru independance does not benefit this group in any way.
PC Contact: Herby
Alllies: Moonmen, Band of Oblivion, Eclipse
Enemies: Merchants’ Union, Angelicus, Sons of Hanish, Elders of Zu, Brothers of Hermes

Moonmen
Violent Rebels dedicated to the destruction of any Zaru Slave owners (especially Ammenite)
Ruler: Florida
Reform: Pro-Reform. they have turned their backs on the ways from before the shadow moon
Maldor: Anti-Maldor. Maldor has done nothing to protect slaves or outlaw slavery
Ammeni: Anti-Ammenite. Sworn enemies of all slave holding Ammenites
Zaru: Pro-Zaru. Sworn to protect Zaru, even from itself if necesary
PC Contact: Seagull
Alllies: Trade Guild, The Plague, Guardians of Ruin
Enemies: Angelicus, Merchants’ Union, Envictus, House Marko, House Lee

Band of Oblivion
Goblin band of blood thieves (This is a group of Violators that have had similar sorcerous experiments performed on them and now need to drink blood to survive)
Ruler: Collin
Reform: Pro-Reform. The look forward to a day when their kind are not ostrecized
Maldor: Anti-Maldor. Many Sorcerers who have made them like this come from Maldor
Ammeni: Pro-Ammenite. They hear stories of Goblins living free in the jungles and swamps and of Ammenite tolerence to their abnormalities
Zaru: Anti-Zaru. The ways of the Zaru seem foreign and exclusionary to them.
PC Contact: Alex
Alllies: Trade Guild, House Lee, House Marko
Enemies: Sons of Hanish, Envictus, Merchants’ Union, Guardians of Ruin, The Plague

The Plague
Ratkin Band of bandits
Ruler: Mary
Reform: Pro-Reform. The want to change the world.
Maldor: Pro-Maldor. The usually targe foreigners to rob
Ammeni: Anti-Ammenite. The see the Ammeni as a threat to everything they believe in.
Zaru: Pro-Zaru. They will free slaves from caravans they rob
PC Contact: Mary
Alllies: Brothers of Hermes, Moonmen, Sons of Hansh
Enemies: House Marko, Elders of Zu, Eclipse, Angelicus, Band of Oblivion

House Lee
Ammenite ruler of the province bordering Sanctum. Wants to establish trade and build relationships to a point where he can send expeditions into the old city
Ruler: Sire Lee
Reform: Pro-Reform. There is not future, but what we build.
Maldor: Pro-Maldor. Ammeni and Maldor can advance together since their goals are so similar
Ammeni: Pro-Ammenite. House Lee is trying to protect Ammeni and move ti forward to a better tomorrow
Zaru: Anti-Zaru. Zaru are just property (or possibly conquered subjects). Why don't they understand that?
PC Contact: Belladonna
Alllies: Brothers of Hermes, Band of Oblivion, Angelicus
Enemies: Guardians of Ruin, Eclipse, Elders of Zu, Merchants’ Union, Moonmen

Brothers of Hermes
Secret sect of Three-Corner Mages
Ruler: Hermes
Reform: Pro-Reform. Hermes feels that it is time to throw off the influence of Zu magic and move into an enlightened era lead by Three-Corner Mages and advisors
Maldor: Pro-Maldor. Three-Corner Mages have always called Maldor their home and defend it tirelessly.
Ammeni: Pro-Ammenite. Ammenites have no competing magic tradition and Ammenites have been known to hire Three-Corner Mages on occasion.
Zaru: Pro-Zaru. So long as their magic is shattered, the Zaru pose no threat to Three-Corner Magic.
PC Contact: Magnus
Alllies: House Lee, The Plague, Merchants’ Union
Enemies: Eclipse, Guardians of Ruin, House Marko, Envictus, Trade Guild

Eclipse
A Shadow Cult dedicated to destroying the last bastions of the past
Ruler: Baal
Reform: Pro-Reform. The past must be banished from our minds
Maldor: Pro-Maldor. Maldor can lead the world into a better tomorrow, if it can let go of the bonds of the past.
Ammeni: Anti-Ammenite. Ammenites are not interested in change or the future, only themselves.
Zaru: Anti-Zaru. The Zaru stand as a constant reminder of the past.
PC Contact: The Shadow
Alllies: Guardians of Ruin, House Marko, Envictus, Trade Guild
Enemies: Brothers of Hermes, House Lee, The Plague, Merchants’ Union

Guardians of Ruin
Ratkin guards of the old city
Ruler: Niel
Reform: Reconstruction. The city must be protected until it can be rebuild, repaired and repopulated.
Maldor: Anti-Maldor. Maldor has turned its back on the past. And that is our last best hope for the future.
Ammeni: Anti-Ammenite. Ammenites are just greedy and want to exploit the ruins without ever restoring their glory.
Zaru: Pro-Zaru. The Zaru celebrate the past and can be trusted with the future.
PC Contact: Ne Joosohn
Alllies: Eclipse, Elders of Zu, Sons of Hansh, Moonmen
Enemies: House Lee, Brothers of Hermes, Band of Oblivion, Angelicus

House Marko
Master Lee's Rival. Wants to undermine Lee and advance his own economic agenda
Ruler: Liege Marko
Reform: Reconstruction. House Marko wants to rebuild the past and return Near to its former glory.
Maldor: Anti-Maldor. Surely, Ammenites are the only people who can see through Maldor lies and treachery.
Ammeni: Pro-Ammenite. Ammenites are the key to survival in this brutal world.
Zaru: Anti-Zaru. The Zaru lost the war, why don't they understand that?
PC Contact: Marcus
Alllies: Elders of Zu, Eclipse, Angelicus, Band of Oblivion
Enemies: The Plague, Brothers of Hermes, Moonmen, Sons of Hanish

Elders of Zu
Total Pacifists
Ruler: Donna
Reform: Reconstruction. Before the Year of the Shadow, the Zaru where a great and honorable people.
Maldor: Anti-Maldor. Maldor brought an end to all that.
Ammeni: Pro-Ammenite. The Ammeni can be forgiven their sins. They just need to see the error of their ways.
Zaru: Pro-Zaru. The Zaru people need guidance. Now more than ever.
PC Contact: Donna
Alllies: House Marko, Guardians of Ruin, Merchants’ Union
Enemies: The Plague, House Lee, Trade Guild, Envictus

Envictus
Current Ruler of Sanctum, runs the local government, striving to keep his dominance
Ruler: "Absolon"
Reform: Reconstruction. He feels he can rebuild the former glory of Sanctums historic past.
Maldor: Pro-Maldor. Maldor is the vanguard of a better tomorrow.
Ammeni: Anti-Ammenite. Ammenites cannot be trusted.
Zaru: Anti-Zaru. The Zaru are pacifist losers. They do not deserve attention.
PC Contact: Gutierrez
Alllies: Sons of Hansh, Angelicus, Eclipse
Enemies: Band of Oblivion, Moonmen, Brothers of Hermes, Elders of Zu

Sons of Hanish
Activists and Reformers trying to peacefully restore Zaru as an independent country again. Or at least restore Zaru freedom
Ruler: Yenobek
Reform: Reconstruction. the past is a signpost towards the future.
Maldor: Pro-Maldor. Maldor can be an instrument of change.
Ammeni: Anti-Ammenite. The Ammeni are blind to the destruction the reap everyday and must be stopped.
Zaru: Pro-Zaru. The Zaru people need to be defended. And the Sons of Hanish will sacrifice all to defend them.
PC Contact: Nebbin
Alllies: Envictus, Merchants’ Union, Guardians of Ruin, The Plague
Enemies: Band of Oblivion, Trade Guild, House Lee, House Marko

Angelicus
Rightful ruler of Sanctum, by blood. Is scheming in the shadows to re-take the castle and his family home.
Ruler: "Absolon"
Reform: Reconstruction. The past is a model for success in the future.
Maldor: Pro-Maldor. And Maldor hold the key to reconstructing that success.
Ammeni: Pro-Ammenite. Ammenites can be trusted, so long as your goals and theirs are aligned.
Zaru: Anti-Zaru.The world was a peaceful place, until the Zaru came and ruined everything.
PC Contact: Bartleby
Alllies: Merchants’ Union, Envictus, House Marko, House Lee
Enemies: Moonmen, Trade Guild, The Plague, Guardians of Ruin

Merchant's Union
Maldor Trade association. they police Maldor merchants and monitor goods coming across the border
Ruler: Ward
Reform: Reconstruction. The Past holds so many treasures to be plucked by wise and skillful Merchants.
Maldor: Pro-Maldor. Maldor holds the keys to those treasures.
Ammeni: Pro-Ammenite. Ammenites are the ones that will be clever enough to put it all together.
Zaru: Pro-Zaru. And the Zaru bring honor and conviction to all they do.
PC Contact: Carl
Alllies: Angelicus, Sons of Hansh, Elders of Zu, Brothers of Hermes
Enemies: Trade Guild, Moonmen, Band of Oblivion, Eclipse

Notes:
1) Allies and enemies are listed from strongest to weakest.
2) Players can feel free to establish prior relationships with characters listed as PC Contact. Just let me know before you meet them what you picture that relationship being like.

Do you know, this scenario is really expansive in scope. Epic, even. You've got threecornerists, ratkin, traders, slavers, vampire goblins and all sorts of weirdos all mixed up. Inspiring.

Eero,
  Thanks for the compliment.
  I have a process.
  Its hard to explain, but it is repeatable and so far has made some good political structures like this one.
  I did this for Lanasia, the KOTOR universe of star wars, a space game I made and I did a limited version for Exalted, CP2020 and Mekton.
  I can try and explain it if you are interested.

You should perhaps write about your process just to understand it better. This is something I've been interested in recently, as my own currently on-going fantasy campaign Alder Gate is all about method over rules - I'm focusing on the parts of play that are not and maybe traditionally cannot be rules-quantified. It's good practice to learn to explain how a method with no rules-backing works.