Going to repost my reasoning from last year:
"This was a tough choice. Historically, I've always sided with the mages, as they were just victims in the first game and mostly innocent in the second. I'm not fond of how Templars abuse their power, especially, after they up and walked out on the Chantry. Yeah, way to represent the Maker by dismissing his Most Holy, guys. I was ready to side with the mages the moment I started the game.
But right off the bat, the Templars sounded like better allies. The first thing your advisors say is that the mages can probably supercharge you with magic to counter the rift, while the Templars can hit it with anti-magic and shrink it down enough for you to close it. That's not really a hard choice. We're dealing with raw, unstable magic that no one has seen before, and you want to pump my body with a ton of magic to hopefully counter it? I'm trying to close the damn thing, not get into an arms race with it. I'd much prefer to contain it as much as possible.
Two, we are fighting demons and weird magic. Who is trained to fight demons and weird magic? Templars. Who is vulnerable to demonic possession and weird magic? Mages. I mean, the Chevaliers are good in a fight, but when you need to fight Darkspawn, you don't go running to them. Plus, we have already seen what happens to mages in areas where the veil is thin, so marching an army of them right up to a massive tear does seem like a pretty stupid thing to do.
Three, Eric Trevelyan was a good Chantry boy who had always heard about the heroism and nobility of the Templars. He would probably have joined them, had fate not had other plans. From a pure roleplaying perspective, he would be much more likely to back the straightforward, pragmatic Templars than rebellious mages.
But all that being said, I was very unimpressed with their debut in Val Royeaux. Casually smacking an old woman is not cool. I was weirded out when I heard that the Lord Seeker had changed his personality almost completely, and all in all, I didn't feel like wading into their self-righteous piety and ludicrous priorities. While leaving the city, Fiona's offer seemed much better.
But when I got to Redcliffe to make the alliance, you know what I found? The mages have signed up with the goddamn Tevinters! Oh wait, did I say "signed up"? I really meant "willingly sold themselves into slavery"! You know, to the Tevinter Imperium, the go-to cautionary tale for all magical corruption. The place filled with so much blood magic, demons, maleficar, and slaves that mages would call it ridiculously overblown Chantry propaganda if it didn't actually exist! Oh, and it turns out, I never met the real Fiona, that was some crazy doppelganger or something, no one seems to really know.
Oh, but it's not that bad, the Magister's son says he is secretly working with another Magister against his father. He's discovered weird time magic, and taken over a massive impenetrable fortress. All I have to do is trust this random Tevinter, walk alone and unarmed into the single most defensible location in all of Ferelden, while sending my spymaster and her best agents into the lion's den through a dodgy secret passage that may or may not exist. And the Tevinters may or may not know about it. All for a few hundred mages so stupid they actually allied with Tevinter, as I can't emphasize that enough. So they can join the Inquisition and slam my fragile mortal body with an unbelievable amount of magic, hoping it won't kill me or trigger something or react violently or Maker knows what else. And if I survive that, they can go on to fight demons, an enemy they are famously susceptible too, and frighten all the common people of Orlais and Ferelden.
That's a bad plan, to put it mildly. Risk vs. reward was skewed so far I just couldn't justify it. So I sided with the Templars, and didn't look back."