The Republic of Keller
Historical Rip-off: Republic of Basque
Inherent dilemma: Practical limits of governance, Rights of governance
In the middle of a kingdom is a city that is small but disproportionately powerful for it's size. Their citizens are known to be disproportionately skilled also, and emigrants have become people in somewhat high places throughout many different societies. The citizens there have had a different system of government since their advancement in the last 5 generations and they believe their system of government is better than the kingdom's. The republic has been secluded from other societies because of their mountainous location, which has kept inter-city travel slow and their military defense easy. Time and again the republic has repelled invading societies, and now the kingdom is finally "asking" the republic to pay taxes, like all the other cities have done for decades if not centuries. The republic strongly believes in their own sovereignty (and superiority) and refuses the crown. The republic beats every invading platoon, even the special guard that is eventually brought in. Finally the kingdom gives up, or perhaps resorts to other/desperate measures as the King's fiscal position becomes dire.
The Army of Keller(Replace with obligatory powerful name that isn't a huge cliche yet)
Historical Spin-off from: Army of Flanders
In a war between Kingdoms is a non-political mercenary army that has never lost a battle, but grows increasingly expensive and starts becoming an unbearable burden for any kingdom, but an unstoppable force that can't be left to the opponents. Eventually the costs become 1/4 of a wealthy kingdom's budget and the army doesn't receive the enormous money they promise. The army lets the opponents run through the Kingdom until the King promises unbelievable favoritism to the army, even special laws for when the army retires from the war. However, the army's hubris has grown so much that the leader doesn't accept, instead demanding the throne. The leader is physically given the crown in a desperate bargaining meeting. Your involvement can protect the king or help the army, either of which determines the wealth of the kingdom's cities (item availability and costs in shops). An outcome that might be too complicated would be to have special side-effects to the plot based on the resulting leadership, such as other groups/people available in the kingdom.
The Pythinonicus
Historical Rip-off: Pythagoreans (I was so clever at renaming these guys, I know)
Historical Rip-off: Harris v. Jones
Inherent dilemma: Institutional Corruption (small scale), Individuality vs. Paternalism
There is a "cult" of fanatics that believe they have found a great discovery of the relationship of souls with the universe, and the new leader has developed the cult's beliefs while leading them into an increasingly precarious situation. The new recruits have become skeptical as their cult moves deeper into desolate territory with a decreasing chance of returning to the safe proximities of nearby civilization. One of them is a beautiful, academically bright daughter to a fairly wealthy relative of another NPC in the nearby city, and her parents have hired you to "rescue" her from the cult and bring her back to a normal life. As she barely reached adulthood the cult has used incremental social pressures to increase her social dependency to the cult and restrict outside influence, and she is in love with the charismatic leader. You have multiple ways of bringing back the daughter, but can ultimately find out that the leader's developments of the religion are the incorrect visions of an outcast who found an obsession to comfort his exile. He has been with the cult ever since he was officially ostracized from a far away city 15 years ago for taking the blame of his wife's mistake. He and his wife were both professional architects and when an unusually strong year for weather caused a noble's house to collapse, the normal death sentence was expected as the noble's favored son had been killed. If you bring back the beautiful cult daughter to her parents without convincing her that the leader or the cult is wrong, she will scream for days and resist with everything but lethal violence, including calling the police and accusing you of kidnapping when she is finally allowed a few hours outside of her room. Depending on your reputation, you may actually go to jail for this crime, as she is a legal adult, or you may be released, based on the "insanity" of the daughter.
The Empiricists
Historical Rip-off: Atheists, Aristotelians
Inherent dilemma: Faith vs. Science
-World Overview
Scattered throughout the societies are people who have seen the races improve their self-awareness, and have therefore grown up to favor demonstrable evidence rather than explanations which have notions of forces at work beyond our "normal" senses. While this is usually just a frame of mind, the people who ascribe to it are usually looking for others like them and may even be forming political networks of their own. Openly discussing it proves to be very difficult as it is heavily in contrast to common "wisdom" and can make someone a social outcast, officially exiled citizen, or worse (scapegoating, mass persecution) depending on the society. Thoughout conversations on this topic, some people hate empiricists for the wrong reasons ("I met a stupid one", "everyone knows that's wrong"), and some people have great arguments against it ("Their complicated 'expiriments' can only result in no discomfirmation of the evidence, which is different than an absolute proof, and doesn't directly disprove conventional belief).
-Plot Possibilities
One empiricist makes a great innovation/discovery as a result of his empirical thinking, but the discovery is contrary to a widespread understanding of souls in his society (for consistency, this understanding might need to be only believed in his society). What's worse, it means the miracle recovery of his King was not due to the help of the shamans, who gained significant influence since that event. Does he fearlessly present it as a triumph of his ideology? Does he try to get political support beforehand, maybe requiring someone else to take the credit? Does he attempt to mesh the explanation with the current understanding of souls, impuning the methodology that led to his discovery? Your help or rejection determine if the society starts changing from magic-based to a more technologically oriented society.
Previously Mentioned Factions I Like
That "Mosaics" faction is incredible. I love the way it parallels an aspect of human interrelation but because it's from a basic soul mechanic, it creates interesting moral vices to those involved.
Dragoling Trader Empire by JFSOCC (basically the Dutch East India Company)