Actor Allusion: Kevin McNally portraying a somewhat portly Father Neptune who's recruited back into action while drunk, gathers your crew, makes reference to Singapore, and serves as a somewhat superstitious first mate? Why, hello there, Mr. Gibbs!
Beam Me Up, Scotty!: Played with when you ride with Paul Revere. Contrary to popular belief, Revere never shouted "The British are coming!" on his Midnight Ride, and the game never depicts him saying it... but one of the first people you alert ends up shouting it to the people in his house after you and Revere pass on the message.
The Danza: Kaniehtí:io, as portrayed by Kaniehtiio Horn.
Also, Lucy's status as a Templar mole, which many people believed since the first game, were definitively confirmed here after being spelled out in the Lost Archives DLC for Revelations that not everyone was privy to.
Shown Their Work: A great deal of effort was placed into a proper non-cliched portrayal of Native Americans, specifically in this case, the Mohawk Nation. A ways into development, the team even realized that they would need help and actually brought on a member of the Nation onboard to serve as a cultural consultant to make sure they got all the details right. Much of Connor's character; especially in how he presents and handles himself are rooted in this research.
What Could Have Been: Aveline was considered as a possible love interest for Connor in the Tyranny of King Washington.