I'm kind of surprised they haven't addressed the fact that for an organisation that believes in individual freedom, the Assassins are engaging in a helluva lot of social engineering.
I do think that the storyline would be more interesting if they put the Assassins and Templars at opposite poles of a spectrum, and it wasn't clear that either of their world views were that great. But I feel like they're actively just turning the Assassins into the embodiment of liberalism. They've already abandoned/explained away the 'Nothing is true/Everything is permitted' creed as metaphorical.
I basically think it's going to be very disappointing if after all that Connor (and the subsequent assassins) just end up fighting for truth, justice and the American way.