Many people who played Assassin's Creed 3 have wondered why scalping is not part of Ratonhnhaké:ton/Connor Kenway's arsenal. Because that what Native American's did, right? Well, not all of them. Which is a mistaken belief that even Ubisoft made themselves.
Kotaku explains that one key figure behind the scenes was Thomas Deer, a cultural liaison officer at the Kahnawake Language and Cultural Centre. He was brought in to help ensure that the Native American culture was portrayed accurately, and that he most certainly did.
At a certain point, scalping was part of Connor's arsenal, and it is true that some Native American tribes practiced it. But not all, like those belonging to the Mohawk tribe, and the associated Iroquois confederation. Hence why the feature had to be dropped.
Though as Kotaku also notes, this revelation also contradicts previous statements from Ubisoft that also claims the feature was removed due to its brutally violent nature.
Deer also asked for a few other changed, like the removing of ceremonial masks since they are an especially private aspect of spirituality.
In the end, all the attention to detail paid off. Apparently, the response among Native Americans who have played the game has been positive. According to Deer:
"For the first time, they actually got to play a mainstream video game that was honest about our culture, featuring a Mohawk hero they could be proud of, and gameplay in the Mohawk language. That's a phenomenal achievement."