The Mage circles have rebelled, believing the Templars have become too strict, too zealous in their duties, and too quick to slaughter those who step out of line.
Besides offering historical knowledge to help build the story, Durand also had to keep in mind the game franchise's back story -- a never-ending battle between the Templars and Assassins.
Because Connor is fighting a completely different war (one against the Templars) than the combatants around him, some of his enemies happen to be dressed in blue rather than red.