Imperator Scottorum wrote:
I don’t really get the whole hullaballoo over an AC in Feudal Japan. Considering the talks about ninjas and Samurai, the Sengoku Jidai is the only era that would make sense to cover, however, I still don’t really see the appeal of such a setting, historically that is an interesting period but how would it work in the AC lore of Assassins VS Templars when the whole war was no more than a power grab attempt by various clans all of whom with an interest in becoming Shogun. The ideas of the Ninja that we have are to the best of my knowledge, flawed and are generally based off cultural/theatrical depictions made after the Sengoku era.
Finalninjadog already addressed that last point, namely that Assassin's Creed has a history of being able to creatively move away from pop culture stereotypes and turn these figures into something both faithful to history and extraordinarily original at the same time. Take, for instance, its portrayal of pirates in the Golden Age of Piracy which indeed, I myself had similar reservations about at the time. Blackbeard is often depicted in media as the archetypal savage pirate from where our main impression of the classical pirate stems from. He was feared as a terrifying, demon and a bloodthirsty terrorist, but in reality, he had a record for mercy and inspiring fear to mitigate conflict was his modus operandi. Black Flag did not simply parrot stereotypes of pirates mindlessly, but framed these historical characters true to who they were as far as thorough research can say on the matter, brought them to life, and made them a rich part of a nuanced story. If anything pirates are just as if not more-so stereotyped than ninjas are (assuming that's what you're referring to by "flawed") because even a series like Naruto can take basic ideas about the ninja and create something entirely original from it.
So I think it is quite presumptuous and irrational to believe that flawed ideas of the ninja in popular culture could be a barrier to incorporating them into Assassin's Creed lore in a way that is both faithful to history and original.
As for your other point that the Warring States period was no more than a power grab by various clans, was that not the same with the era Origins is set in? The Ptolemaic dynasty was a failed state at this point having experienced a century or more of coups, civil wars, and assassinations by siblings, parents, and children among the ruling family. There was no "good" side to this conflict. Even the assassination of Gaius Julius Caesar by the senators is controversial in that while they believed they were defending the republic against a dictator, Julius Caesar—not that I support him—was the populist leader favored by the common people who saw the senators as elitist oligarchs. Who says that there needs to be clear factions aligned with the Assassins and Templars for the setting to be incorporated into Assassin's Creed lore? If anything, it'd be an opportunity to weave a narrative with some complex layer of shifting allegiances. We already see this with Assassin's Creed: Memories's writing of this period.