So, I'm chiming in late -- but about the mages and why anyone would ever want to not help those poor, downtrodden souls...
I think one of the main themes of DA (and it does have themes -- DG is first and foremost a writer, after all) is that
the person who has power will abuse it. The historical Inquisition (which became the Templar order) rose up in defense of the everyman who were being systematically abused by mages (not every mage, surely, but enough to form a stigma) to the point that people began to abandon their normal lives and devote themselves to protecting the defenseless against abusive magic.
As of 9 Dragon when we enter the scene, the mages have been subdued and are being squeezed so tight that the oppressed are now the oppressors. They're packed into these Circles and treated so badly that the whole place is like a powder keg that only needs one spark to blow completely out of control. It's a bad situation. Let's not forget that they're *policed* by an institution that profits greatly from the making and selling of potions and magical artifacts. It's a recipe for mismanagement (to say the least). But because the Chantry has power, the Chantry abuses power. Because the Imperium has power, the Imperium abuses power. Mages with too much power will abuse their power. Dwarves with too much power will abuse their power. Etc. etc.
When the two factions break apart in "Asunder" there's definitely need for a third faction that will be a voice of reason. Whatever your definition of reason is. Just take a look at the DAIII discussion forum and you'll see that not everyone agrees on that point. But regardless of whether you're with the mages, templars, both, or neither, the conflict will set the stage for good gameplay.

Me, I'm probably going to replay this thing all to pieces and explore every point of view at least once.