While Yuna certainly helped spread the legend of Jin being the spirit of a vengeful samurai returning from the grave to put the invading Mongols, bandits, and traitorous Straw Hats to the sword, even though she knew better, Jin himself unknowingly adds to it. With every Ghost weapon he gains, and every technique he learns, this lone samurai, whom many believed to have perished at Komoda Beach with the rest of the island's samurai warriors, always shows up in the people's times of need, single-handedly takes on entire garrisons of enemy forces and brutally slaughters them with legendary weapons, silently darting in and out through the smoke to slay enemies before they know he's even there, or cutting several foes down so fast they couldn't so much as even blink before they hit the ground dead, all while donning seemingly invincible armor, only to then disappear just as quickly as he showed up, guided elsewhere by the wind. To the people of Tsushima, Jin really is a supernatural entity returned to claim vengeance on those who would harm them.
At one point, Khotun mentions slaughtering his favourite horse and feeding her to his men because she broke a leg. While this might seem callous at first, a broken leg would've meant a slow, painful death for the horse, as she needed the pressure on her hooves for her circulatory system to work properly. By granting the horse a Mercy Kill and feeding her to his men, thus preventing her body from going to waste, Khotun had acted in a way consistent with the Mongol culture's respect for their herd animals (not to mention the common-sense considerations of feeding a hungry army on campaign).
Clan Sakai's armor is based on Honda Tadakatsu's "the Warrior who surpassed Death itself". It allows Jin to kill five enemies in stand off and terrify the others, which kind of fits how Tadakatsu was claimed to evade any injury during battle and made the opposition run when they saw his antler helmet.
Jin's outfit when meeting Shimura and learning of the disbanding of Clan Sakai is the ronin one, as he is no longer samurai.
Why is Lord Shimura so uncaring about casualties when retaking his castle? The bulk of his army is from Yarikawa, a city that rebelled against him twenty years previously. Every one that dies today is one that he doesn't have to worry about fighting against him later.
The story itself explains the difference between historical accounts and the game's account of events. Jin's comment to Khotun Khan "No. You will be forgotten." explains why history never mentions him. Additionally, Jin's own accomplishments are deliberately suppressed by the Shogunate. This also accounts for the difference in the Battle of Komoda Beach; in the game the battle takes less than a hour due to the Samurai charging into the Mongols. Historical accounts state the 80 samurai managed to hold off the Mongols for the whole day, slaughtering hundreds and holding back thousands. This is because the Shogun wants to reinforce the Samurai Way and suppress the notion that the ruling class wastes lives needlessly.
Shimura choosing the Sakai cemetery as the location for his and Jin's final fight has certain significance. Just prior to the fight, they paid their respects and it is very possible that Shimura was praying for forgiveness to Jin's parents for what he was about to do. And if he did kill Jin, he would have the convenient excuse of being able to bury Jin with his family as a Sakai even if he was officially declared a traitor.
Jin being able to adapt and incorporate the techniques of the legendary heroes of Tsushima isn't just because he's a Master Swordsman, but also because of the scale of his deeds compared to theirs. Each one of those heroes fought in small-scale conflicts that affected the island as a whole, but nothing on the level of an invading army that also threatened the mainland. Jin's legend as the Ghost of Tsushima who almost single-handedly repelled the invasion makes him a correspondingly greater legend than any one of them, and accordingly, he is able to adapt their techniques because he is a Living Legend, worthy of their abilities that made them famous in the first place — and correspondingly, the fact that he can adapt the power and techniques of multiple legends into battle in the present day makes it easier for the locals to believe he's something otherworldly, which might actually be the case, given how well Jin can utilize each hero's unique weaponry and skills as if they were his own. On a side note, Jin is destined to become a bigger legend than even he realizes, as his deeds and the creation of the Ghost Persona, along with how effective it makes him as a Terror Hero, is hinted to inspire the eventual creation of the Ninja— a popular figure widely recognized in the modern day even outside the shores of Japan.
Yuna and Kenji's tales are both started and resolved in the second area of Tsushima opened up during Act 2, as opposed to the rest of Jin's allies whose tales stretch throughout all 3 actsnote Discounting Norio, who isn't introduced until after Act 1 is finished.. This seems strange at first, with two of Jin's closest allies having tales that are relatively quickly introduced and resolved, as opposed to the mini-arcs that the rest of his allies possess, but it makes sense with the way the Act 3 main story proceeds. Yuna is the one to scout out the 3rd area of Tsushima while Jin is imprisoned, and identifies the Khan's hiding place and the best location for Jin and his allies to regroup and launch an assault on it from, not to mention coordinating with the allies locked out of the region to mount a simultaneous assault on the fort occupying the checkpoint blocking them from entering. Meanwhile, Kenji manages to secure a battery of Mongol artillery that is the cornerstone of Jin's plan to sink the fleet and destroy the Khan's goals of conquest. In contrast to Yuna and Kenji doing part of the legwork Jin had to do mainly by himself throughout Acts 1 and 2, Masako, Ishikawa and Norio spend their time in Jogaku Temple training the surviving soldiers from Yarikawa in how to be a more effective fighting force. This is because their own tales are still unresolved at this point, thus they are distracted by their personal troubles and not able to contribute as much to Jin's efforts stop the Khan, whereas both Yuna and Kenji are 'free' from their woes and can devote more effort into helping Jin proactively, rather than passively.
In a brilliant case of gameplay foreshadowing, it's a subtle detail, but notice during the pre-fight cutscene for the Black Hand Riku duel, Riku is the only boss that actually speaks during the cutscene when he agrees with Jin that it's not a fair fight... only for him to catch the player by surprise during the first sword clash, and launch an offensive immediately, instead of recovering from the clash like all bosses do. It definitely was NOT a fair fight...
Jin is probably the in-universe creator of ninjitsu with Yuna's help. His study of stealth, Combat Pragmatist techniques, and other techniques are meant to invoke traditional shinobi practices from film as well as real life but we see the origins of many. This includes, for example, wall climbing equipment made by Taka.
It's subtle, but on the Playstation controller, the button symbols to select the various styles are symbolic of the specific type of weapon each style is favoured to counter. The Shield is selected with the circle button, the X button matches up well against pure blade-wielders (who have a unique sub-class of enemy who uses Dual Wielding and who typically holds both blades in an 'x' fashion), the Triangle button is indicative of the point of a spear head, and it's matched up against spear-wielding fighters, and the square button is for heavy-type enemies, who are sometime seen using square-headed hammers and square-shaped tall shields to fight Jin.
A massive storm hits the Mongol fleet right before you assassinate Khotun Khan and derail his invasion of Japan. This is almost certainly a reference to the "Divine Wind" of Japanese history that drowned 14,000 Mongol soldiers and derailed their invasion. Presumably, this is how history will interpret the Ghost's victory.
It is often said that the Mongols invasions changed the Samurai warfare forever; this can be explained by the Samurai, realizing the tactical inferiority of the "honorable" way after seeing how effective Jin's methods are, then gradually getting more and more pragmatic over the centuries with the few that refused to change dying out (think natural selection). This later culminated in the Sengoku Era, where pragmatism was pretty much the norm with trickery, espionage, and assassination being extremely common practices, and not even mentioning the arrival of rifles which changed the Samurai warfare even more.
Introducing the wolfsbane poison is something that Jin thinks was necessary but almost got turned against the mainland. How much will warfare change because of the use of an effectively medieval Weapon of Mass Destruction?
There's a certain level of Combat Pragmatist among Lady Masako and Ishikawa plus hints about Jin's own father. We also find that most of the mainland samurai are less concerned about honor and glory than the fact Shimura utterly botched the defense of the island. This implies that Shimura is actually Lawful Stupid even among the samurai of the era and that Jin's disgrace was entirely due to his inflexibility. If Shimura had been more like other samurai, then his legacy wouldn't have been utterly destroyed.
If Lord Shimura is spared, his life is still ruined. His condition for remarriage and having a new family was if he was able to kill the Ghost, which he wasn't able to do. It's very possible that with his utter failure, he's going to be Driven to Suicide as an alternative to dying heirless and in disgrace.
It will be a little less than eight years until Kublai Khan (or one of his relatives given the settings Alternate History) sends 150,000 soldiers to conquer Japan again. It is a much bloodier and destructive conflict than the previous one.
Assuming Japanese history continues on the way it does in our world, the samurai who favor defending the people will be defeated in a month-long civil war against the absolute loyalists during the Shimotsuki Event. This will weaken the Kamakura Dynasty, resulting in the loss of the Emperor's support before being overthrown. Shimura as a die-hard loyalist who preaches absolute obedience will contribute to the end of his own cause.
