It was originally intended for Daniel Cross Spoiler:to have a final set of dying words when Desmond assassinated him. His last words were for Desmond to kill him as the pain of the Bleeding Effect had overwhelmed him, and was driving him insane, claiming that he constantly hears voices asking to be released.
Originally, Conner was going to have a Chain Blade, which, according to concept art, was going to act as a long-ranged hidden blade. The weapon was not used as the teams "felt it to be heading down too much of a fantasy route." The chain blade was replaced with the real life Sheng Biao/Rope Dart.
Connor was originally going to be able to scalp his opponents, possibly similar to how he skinned animals he caught. This was removed when they found out that the Mohawks rarely (if ever) did this, coupled with the fact that the mechanic was too brutal for Connor's character and the game.
Early on in the pre-production of "The Tyranny of King Washington" DLC, Conner was going to get a love interest in the form of Aveline de GrandprÃ© from Assassin's Creed III: Liberation. The idea was later dropped when the developers saw how the characters' motivations and personalities were too different from each other.
There is an Easter egg referencing Alice in Wonderland when entering the Grand Temple. Shaun will say "In another moment, down went Alice after it, never once considering how in the world she was to get out again."
If you go to the manor, stealth on the outer walls, and whistle, a turkey will appear near you. If you put in the Konami Code, the turkey will put on an assassin hood.