To all those who care, here are my thoughts on what will be happening within the series.
Obviously, there are multiple timelines that are possible for the series to continue on, many people like to theorise what could come next. I believe, we've already been told, or given clues. For example in Assassin's Creed II, 'The Sanctuary' (http://assassinscreed.wikia.com/wiki/Sanctuary) /held the armour of Altaïr Ibn-La'Ahad, but it also had statues of other very important assassin's too.
From left to right, the statues represent, Qulan Gal, Darius,Wei Yu, Altaïr Ibn-La'Ahad, Amunet, Iltani and Leonius. Given that Altaïr has been the main protagonist in 3 games and made appearences in 2, it is a possibility Ubisoft probably won't make another game featuring him as the main protagonist. That leaves us with 6 other definite storylines that the game could follow. There are also many novels written by Oliver Bowden, that have many other assassins in them, such as Aquilus Numa Al'Khamsin, Arbaaz Mir and Nikolai Orelov . Not to mention their mentors and children born into The Assassin Order, like it was done for the Kenway Family.
At the end of Assassin's Creed III, Desmond sacrifices himself, to save the world. It is then found out that the people at Abstergo Industries were able to recover blood and saliva from Desmond's body, allowing them to continue research into his ancestors. As done with Assassin's Creed IV: Black Flag. Which may yield more of Desmond's ancestry.
In Assassin's Creed: Liberation, the main Protagonist is Aveline de Grandpré, who isn't an Ancestor of Desmond Miles, the Ancestor is only known as Subject 1. This proves that the Assassin's Creed series will not be souly generated along the line of Desmond's ancestors.
Game directors have currenty stated timelines and places they would like to see the series go, these include, Ancient Egypt, Ancient Rome, Feudal Japan and many more. They believe that by the end of the games production it would be possible to have 30+ games.
Recently, the Teaser Trailer for Assassin's Creed Unity has been released, and from analysis it's safe to say that it will be set in The French Revolution. Another game is set to come out this year too, it is thus far known as Assassin's Creed Comet, which is possibly going to be set in Ancient Rome, possibly featuring Leonius, but that has not been stated. Linking back to my previous statement, we have been told, or at least hinted at.