User blog comment:Mr Ibn-La'Ahad/Assassin's Creed IV:Black Flag modern protaganist/@comment-1153722-20130301072809

Putting William or some other Assassin into the Animus would be a bit anti-climatic and would diminish Desmond's importance. (We also don't have 100% guarantee that William is descended from the Kenways since Desmond could in no way have known this. The Kenways may just as well have been from his mother's bloodline.)

The pivots at the end of Assassin's Creed III served as a plot point to lead into the next game. Abstergo retrieved Desmond's body and uploaded his DNA to the Cloud using the Animus. No doubt the game will further expand on this.