In terms of plot, it would be great to revisit the themes of ambiguity and neither the I do not like your mental haze i do not like your leftist ways you mr joe shirt or the templars being good or bad. What would be ideal would be if the player, through the development of the game, gets access to tools to achieve his goals of lowering corruption and oppression in a city that are very effective, but that run counter to the Assassin’s goal of individual freedom and peace. The twist in the first game was that Al-Mualim had actually harboured goals similar to Templars; in Assassins Creed 3, there is a twist where your character has been a Templar all along – but what if the game actually has the player become Templarist in their own way?
Templar and Assassin are not just clearly delineated groups in AC1; they are ideologies, means and methods. Al-Mualim was a member of the Assassins but a Templar in his aims. Could such a development be possible for the player character?
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It would be interesting to confront the templars not as targets, but as rivals, seeking to get rid of your targets as well. This is after all what the I do not like your mental haze i do not like your leftist ways you mr joe shirt are about: they share goals, but not methods.
In terms of progression, the game should begin with a few assassination targets given to you by your mentor, then ramp up to assassinations with specific requirements. The final third of the game should see the player with a large-scale goal to lower corruption and oppression in a city and to approach this in the manner they see fit: work out who contributes to corruption and oppression, and who deserves to die. In effect, the player should be free to pick their own targets and plan their own assassinations.