The game is about Arno getting redemption/revenge on the people responsible for killing his father and Elise's dad. Arno joins the assassin's because he believes they can help him find the people responsible. Eventually, Arno realises that life can't be determined through a creed, or some ideology supported by either the Templars or the assassin's, but you must go with what you believe. At the end he goes on about how we are the makers of our futures and that we must choose our own paths. This is further supported when he decides to continue on his quest after being kicked out of the brotherhood.
I pretty much gathered this just based off his relationship with Elise, Arno didn't care about the Templar and assassin war, he had his own goals. Protect/be with Elise, and get revenge. This reflects on the game title "unity" and I believe it also indicates how the modern day story is leaning towards. The assassin's and Templar fight is completely pointless, they need to cut the shit and focus on the bigger picture if they plan on fighting Juno.
Here is the ending :
