Everyone is crying "Mass Effect 3 All Over Again!" for Assassin's Creed 3. However, I disagree. AC3 dropped several hints towards AC4 as well as setting up an interesting blend of modern and ancient conflict.
So when Juno is released and Desmond is "killed" this sets up possibly the most epic villain the games could conceive. An alien being from the First Civilization with seemingly godlike powers and intelligence. Not to mention Desmond asks his father about the possibility of calling a truce with the Templars (Likely now that they'll have a common enemy and Vidic is dead). Then there is Shawn's question regarding turning the Animus back all the way to the time of the First Civilization. We might get more answers and really see what the truth is and how the humans fought the FC back when they rebelled. Ubisoft never said that this was the end of Assassin's Creed. They only said this was the end of Desmond's Story.
And even then I think it was... okay. Desmond's story had reached a logical conclusion.
AC1: Setup of Assassin and Templar conflict
ACB: Finding the Apple
ACR: Coming to terms with his role
AC3: Getting to save the world and die a hero.
As Desmond points out it may look bad that Juno is released upon the world. However, as he says they'll figure out a way to deal with her. He will not stand to see the world burn and have the whole cycle repeat itself. I really think the ending was actually not nearly as bad as people are saying and that it's no more of a WTF moment then the first 4 game endings were. I mean, we all remember how the first game ended, right?