I allied myself with the mages. When I chose I was not really paying attention, and it was not until later that I realized I had randomly chosen something that would be a big game changer. (I probably would have allied myself with the mages anyway)

I have played both missions and while I loved having a sort of Dorian centered mission, I think I liked the Templar mission better. That is simply because when I played the mage mission I spent way to long trying to navigate the dungeon and find all the things that needed finding.

I've done both but prefer the mages. Killing Fiona ripped a whole in my heart when I sided with the templars, there's no way in hell I can do that again. She's one of my favorite characters!

Mages. Although I would like to side with the templars just to see how it goes down.
I always help out mages when I can in Dragon Age xP

Back in DA2, I never sided with the mages after my first playthrough. But then DA:I announced you can have your Hawke in game I got so excited to see Anders agian, but that made me feel bad how all those other times I played; I made him hate me. So now I make up fro the times by saving mages