Dragon Age II tells the story of Hawke, how he rose to Champion, and what happened to him, It shows his arrival to a new and foreign place, and the circumstances he forced himself to rise above. I enjoy that the story is slightly more erratic, the hero is never called the "Savior of The World", or he's the "Chosen One", or "The Ring Bearer", but is faced with events that threaten him or those he holds dear, and he rises above them.
Throughout the game there is very little of the universe's favorite "punching-bag-orc-replacement", The Darkspawn, and instead a large portion of the game focuses on, or at least revolves around the conflict between the Chantry and the Mages.
The Templars are a group of righteous warriors, hired by the Chantry, the largest in game church, both of whom control the Mages, because being a mage in this universe means there is a chance to become possessed by a Demon.
Usually this involves: becoming something out of Dead Space 2 or Silent Hill, spilling more blood than a level in Gears of War, and being as vilified as a Justin Bieber fan in a crowd of death metal fans.
So you have this powerful and religious order of knights who are suspicious of another group of people with lots of potential for change, whether violent or peaceful, and most knights want to repress them as either way it might hurt their power structure. It rings vaguely of McCarthyism, in that you are always suspicious that they could be the enemy, if not today, then tomorrow.
Now, any of the metaphors that could be made about religion in this game could be accidental, or could be intended, there is really know way of knowing. For example, one of the races in the Dragon Age universe, the Qunari, are a race of pious, magic hating, secretive, and misunderstood people, who happened to be much more technologically advanced than the rest of the world.
Which sounds vaguely familiar to medieval Arabics who had invented many advanced technologies for that day and age. (I've only read a bit about medieval Arabic technology, enough to know they were very advanced, if you're interested, find out more online)
First, lets say that the Qunari, and the Qun, their religious doctrine, represent Islamic faiths, seemingly aggressive but merely misunderstood and with a few radicals and radical leaders. Then that the Templars and the Chantry are their real-world counterparts, the Templars and the Catholic Church, repressive of change and one of the largest religions. All we have left are the Mages, which could represent a number of things.
The first relationship I see is that being a mage could be a metaphor for being homosexual. They are condemned as demons for who they are, they are born that way so they say it is impossible to change, and they are…vulnerable to being possessed by demons and possibly possessing other mages? I'll admit, the comparison is a stretch at some points.
The theory seems most sound is at one point in the game when Hawke talks to Anders, a mage, companion, and activist for mage-rights who tells of how his lover, his male lover no less, was killed, or worse by the chantry.
It's just something that struck me while I was watching, and while I would not recommend to take it too seriously, as I already have, I would recommend that while playing the game, you keep an eye out for when parallels between the Chantry and Mages, and the real world pop up.