Who is the big bad?
Corypheus
How does the mages/templar conflict get resolved?
You side with one of them, the other side is corrupted by Corypheus.
How many templars joined the red templars?
If you support the templars just the ones who are corrupted at Kirkwall, if you side with mages almost the entire Order.
How many mages go full blood magic?
Grey Wardens mages and the Venatori (mages from Tevinter that follows Corypheus) use it, if you side with the templars, the rebels convert to the Venatori.
Why can the player close rifts?
He stopped Corypheus at the conclave, he picked up a magical orb and gained the power to close the rifts