All depends, i'm all for mages having their freedom or whatever but Templars perform a service. What happens if a mage goes crazy, starts using blood magic on everybody and their little pets.. would you sit there going "Well, as long as their free.." or would you be going "damn! Templars would be really useful right around now.."
On sheer principle? Mages. They've been treated as living weapons for centuries and deserve a chance to live their own lives.
Practically, though? Templars. As bad as the Chantry gets, they've got a point about mages going out of control or losing themselves to the denizens of the Fade.
If the mages had some organization capable of policing themselves, then I'd be all for them. The Chantry needs to be taken down a couple pegs or they'll never live up to their ideals, but anarchy is not exactly an improvement.
"I am a warrior. Let the battle be joined" http://images.wikia.com/transformers/images/4/40/BWDinobot_decision.jpg
I enjoy playing as a mage but since I'm not one in real life I'd side with the templars. Mages have way too much power over everyone else. Instead of just keeping them "under control" they should be exterminated. No mages, no problem, right?