Well, I see this thread is already populated by the usual suspects....
Anyway, IMO Bioware did a much better job presenting reasonable incentives for choosing either side than in previous games. No longer do I feel like a fascist when supporting the templars, or like "helping dangerous people run amok" when supporting the mages. I think the choices are presented in a mostly well-balanced way, maybe a little weighted in favor of the templars with all the mages who said good things about their time in the Circle and with the pro-mage viewpoint being less present on-screen overall, but that's ok.
If I still have a hard time choosing the templars, that has more to do with the fact that the mages and templars represent opposing themes where I have a strong personal predisposition - namely, the higher degree of individual autonomy magic makes possible, against the element of social control that would always try to chain the autonomous individual on the pretext it's dangerous for the community. Also, the templars give off too much of a "religious police" vibe, which isn't just bad in itself but compounds the issue. So, most of my games will be mage games.
From a storytelling viewpoint, I think that "In Hushed Whispers" is a more compelling mission than "Champions of the just". On the other hand, I haven't seen Calpurnia yet but it appears she's more compelling as an antagonist. So that balances out. Also, both sides made stupid decisions so that also balances out. The mission design sequence favors the templars though, since "Champions of the Just" becomes available earlier than "In Hushed Whispers", and people who want to continue the main plot may choose the former without being aware of the fact that there is another path they're closing off. That almost happened to me in my first game, in spite of knowing about the fork.
As for the final result of a pro-mage storyline, I remember the words I put into my Warden's mouth: "Maybe if we save their asses, they'll sing a different tune about mages." And so it went. I suspect that in the aftermath, the mage community has every interest in keeping abominations from appearing, and contained if they appear, just as they did before since I think it's reasonable to assume your average mage would rather be dead or tranquil than possessed, and also out of a need to prove themselves in that regard as well. Only they don't have an order of religious fanatics ideologically predisposed against magic breathing down their necks. Notwithstanding the fact that many individual templars appear to be ok people, I can only see this as an improvement.
What do the pro-templar epilogues look like?