Counter argument for the mages.
The Setup: Common knowledge of the time is that Mages are at war with Templars, who are rebelling for freedom. The Templars have openly defied the Chantry and decided to meet the mages in open war, thus causing all sorts of collateral damage. So from the outset, unless your character is VERY pro chantry or anti-mage, personal bias shifts to be in favor of the mages before things have even started.
The Inquisition's first goal is to seal the breach, and thus the conversation of who to side with is first presented. Mages who understand the veil, fade, and magic. Or the Templars who are adept at anti-magic. You know the mark is magic and that it has the power to close rifts, it just needs more power. Who is going to provide more magical power? The real risk, which is brought up, is who will be willing to even listen to you. So here we see again, the bias is for the mages, as you need the mark to have more power. SO at the very least they appear as a viable option. Cullen makes it sound like the Templars would be more reasonable and easier to approach... but when it comes time to meet them, they're dismissive and claim you're unworthy. Fiona by contrast offers you a friendly invite.
So to recap to this point. You know mages are fighting for freedom, your mark needs more power, the Templars have told you to ****** off, and The mages invited you to parlay. (The freedom part is really only important to those characters who view it as a reasonable/righteous cause worth standing behind). Upon arriving in Redcliffe, even before the gate is open you realize there's something strange going on with the rifts. After sitting down to parley, you quickly realize there's something fishy about your invitation (since she claims she never gave it) and worse yet, a Tevinter Magister has claimed ownership of the rebel mages. He then explains how he plans to have them work in servitude, and assist in Tevinter's war effort, and how he has essentially claimed the Castle for himself. When you later meet with Dorian, he informs you not just that Alexius is a Tevinter supremacist who is very interested in your mark (implying he knows more about it), but that he has used time altering magic that helped him claim the rebel mages. To top it all off, on your way out, nearly every mage practically begs you to help them, and save them from the Tevinter Magister.
So when the decision time comes; Do you leave the Tevinter Magister? The who has a small army of mages, knows about your mark, can alter time, and threatens the very citizens you just spent all that time protecting. (partly as a means to earn a name for yourself as being an inquisition who protects the people where people in positions of power have failed). He would also be a stone throw away from your current HQ Do you want a known enemy that close? While you could say this is really a matter for the Nobility to handle, that's not entirely true. You sent a forward party out into the hinterlands, you were saving and helping the general populace. The reigning power failed to protect his citizens, and your fledgling Inquisition is starting out in a bad position with the Chantry branding you a heretic. Your Inquisition NEEDS this publicity, and you've already made your presence known to those people, if you fail them now your inquisition is off to a really bad start. So within the context of the game world, it's hard NOT to side with the mages, most of the reasons you'd choose to side with the Templars is based on things that happen afterward, where you can look back and claim it made a better story or a more compelling villain.
OOC reasons; (to touch on the cameo factor) Yeah Samson got his start in DA2, which as much as I enjoy the slave turned leader who might be brainwashed, we got to see Samson at his lowest, a bum in the streets asking for dwarf dust. There's a history the player has with him but there's also one with Cullen, as he remembers Samson. The story of him helping that Tranquil who was willing to die rather than betray Samson was heartbreaking and humanizes him. He's well aware that what he's doing is morally wrong, but he was already at rock bottom, and wanted to feel powerful and have some meaning in his life again. It's not redemptive, so much as it is "die with dignity" which is a reason (to me) explains why/how he would be willing to go thru with so much destruction and be willing to be the vessel knowing full well he wouldn't survive the whole ordeal.
Going forward in time also adds to the whole "This **** is weird" book. It's one of those miracles that would be exaggerated when people talk about the inquisitor, except it actually happened. It adds to the whole "chosen by Andraste" (if that's the path you're going with). It's also a bit of mystery, you don't really get told Cory's plan... you ask about what's happened and people inform you of things like a demon army and such. You're left to piece it all together as the game progresses on, like when you see the wardens summoning demons.
Mostly, for me at least, context is a huge thing for my characters, and the context that is set up in Inquisition has me choosing the mages every time.