Connor's story has probably been left like that due to the 5 confirmed DLC's
Desmond's ending sucked, I'm tired of game protagonists just being killed off. Yes we knew this was the end of Desmond's story, but come up with something more original than "just kill em off!"
And the way it happened, the lack of emotion from his fellow assassin's, the sudden reappearance of Minerva and lack of info on what Juno is apparently going to do, was weak.
Also I know we finally got Daniel Cross (Excellent) and Vidic was killed, but where were the rest of the modern Templars?
For a group were been at battle with for the last four games, they were suspiciously absent in this one!