I really liked the premise of the pro-mage quest because you actually caught a glimpse of what the future would be like in a years time, should Corypheus succeed with his plans, this added an extra layer of urgency to the game because you've seen what will happen if you fail. It's a shame we didn't get to see what became of Cullen, Josie and the other companions though... I bet it would've been heartbreaking given the absolute state poor Leliana is in when we finally find her.
The pro-templar side was also a good one, loved the Fade sequence and I actually found myself having more sympathy for the templars than the mages this time around, which is a first!
I don't think I have a favourite, although it looks like my canon playthrough will be pro-mage again just because with pro-templar you don't get that glimpse into the future so it doesn't feel quite as urgent in the pursuit of Corypheus, plus going pro-mage gets you extra Cullen content and a little added angst to the romance, which I find preferable. Also, I kind need to keep Fiona alive if my Warden is off trying to cure the Calling, she could be useful in her research and I want her to have any extra edge available... I can't stand the idea of her being kept a part from Alistair due to it... sh*tty Abyss quest making me change my DA:O canon! *Grumbles*