Faction I'd like to see:
A true ninjutsu organization, no not the flying ninjas of hollywood but the true incarnation as those who followed the way of the shadow in Feudal Japan were considered outlaws. I'd like to see a group of assassins that killed for hire and lulz, as ninjutsu is not a martial art but an independent art of warfare. Where intelligence is more highly regarded than any weapon. Their "uniform" would be a cross between the Chinese Stealth armor and with a little raider influence infused, since they are essentially "evil." They can make improvised stealth boys at campfires with the right items of course. They could trade in illicit drugs such as jet, turbo, psycho, cat eye, etc. With the art of deception and espionage they can control politics of the region using intimidation, subterfuge, and sabotage. Using strategy to lower the enemies ability to fight.
Weapons can include poison darts, poison spiked knuckles, the infiltrator/perforator, anything with a silencer, the rear naked chokehold, smoke bombs, shurikens, etc. Trained to kill in stealth, hide bodies and misdirect, and are given a special grappling hook to climb up to rooftops. Climbing claws for trees and what not. They can be given binoculars, night vision, heat sensor vision, listening devices, bugs, trackers, anything the CIA would essentially use to gather intelligence.
It would be a perfect synergy of modern and ancient tools used with the philosophies of ninjutsu.
Their philosophy can rival that of the Dark Brotherhood, as I don't think Fallout has a faction built on the foundations of assassination.
Special reward perks for sneak can be implemented, through their faction side quests. Silent running, sneak mode speed increased tenfold, night vision/heat sensor implants, silent kill (100x backstab) with any weapon, etc.
Their bible can be the "Chinese Army: Special Ops Training Manual." Also, should be able to become the leader of this said group of silent killers of the wasteland.
There are a plethora of ideas to make this group deeper with the use of special tactics, disguise/impersonations as other factions, masters of breaking and entering techniques, excelling in concealment of weapons and such.
Gaining rank should be hard, and ultimately leading to obtaining the original Chinese Stealth Armor complete with the stealth field and becoming the grandmaster/Lord of said legit ninjas of the wasteland.
Also, being a part of this group should strike fear in the hearts of the settlers and add a certain mystique through their dialogue. Certain rumors they can talk about this group as a myth or them being non-humans and such.
Their rivals can be the Brotherhood of Steel, as they seem like the samurai's of the wasteland. As in history, samurai and ninja did not get along.
Also the members can spew out random dialogue such as "Walk always in the path of shadow," "Music is the silence between the notes," "Blending in is as good as being invisible," "Silence is golden," "show “lies” as “truth”, and conversely, “truth” as “lies...” blah blah you get the point.
Fallout 4 should teach the true beauty of SNEAK.
Bethesda can even go deeper by going to the Iga-Ryu Ninja Museum in Japan to get a better understanding of the culture. I'm sure the CIA uses tactics employed from this era as there are no schools that teach the true art of ninjutsu.
Damn smoothskins at Bethesda better be reading this.