I sided with the mages my first playthrough not so much for mage vs. templar reasons (the choice isn't even set up as 'who do you like?') as meta and RP reasons.
Meta-wise, I was curious as to how the game would present and reflect the mage scenario. Rather than hear about it first from people who pick it for ideological reasons, I wanted my own perspective on what was involved in a mutually exclusive route. I will happily pick Templar for another playthrough, but I wanted to see the mage route with my own eyes.
RP-wise, though, even though I am playing a mage who was sympathetic to mages in general (though my mage is not a revolutionary), the real RP reason was to investigate the cause behind Justinia's death- and figure out what was behind the not-Fiona who invited me to the real Fiona. I went to Redcliffe before making the choice, and the entire imposter angle plus the revelation of time magic used to recruit the mages made the Magister an obvious suspect of involvement. Combine that with the out of character (suspicious and worth investigating) but rude handling by the Templar Commander earlier, and she chose the more sympathetic and clearer line of investigation.
Always mages and alliance because you will have full support and loyalty...Fiona unfortunately cant be removed but she is far better and experienced then Vivienne, and she have more indluence so it is better to make alliance not force them.
coughsoldherselfandthemagesintoslaverytomaleficarcough
Sorry, something in my throat. I think I choked on Fiona's unapologetic fail.