In this game, a woman comes to you when you're out of the Animus and tells you that the head of Abstergo Industries, Olivier Garneau, had a meeting in Chicago (where Watch Dogs (2014) takes place) but hasn't returned. In one Watch Dogs side mission, you kill Garneau. Should the player then decide to profile Garneau with Aiden's phone, his descriptor even reads "Targeted by the Brotherhood" clearly referencing the Assassin brotherhood in these games. This puts both games in the same universe.
All of the subtitles in the game are written with every noun capitalised. This is because this is how English used to be written during the 17th and 18th century.
Edward's voice actor, Matt Ryan chose to voice him with a Mancunian accent (a dialect of English spoken in the English city of Manchester.) However, after the game developers heard his natural Welsh accent, they asked if he could voice Edward using his native Welsh accent. As a result, Edward's back story was re-written to have him born in Swansea, Wales to a farming family.
A certain document found on an Abstergo computer lists the time eras that Desmond had Assassin ancestors in. With many of these having been done (Crusades, Italian Reniassance), it is thought by players that the other periods listed will appear in future games. Their theories are supported by the fact that the French Revolution was on the list, and has been the setting of a game: Assassin's Creed: Unity (2014).
Before Edward's captaincy, his ship was called the 'El Dorado' and sailed in the Spanish Treasure Fleet. He then rechristened it the 'Jackdaw', after a small bird of the same name.