The thing I don't like is that they let you do a bunch of the Mage's quest before committing to them, but not the other way around with the Templar. So not only do you know more of what you're getting yourself into with the mages, but they dangle Dorian in front of you, and make you feel like a jerk for leaving the mages to Alexius. And the war table encourages you to go to the mages first just because its free (at first), while the Templar cost power.
Yes, the setup for the missons is extremely unequal and made me annoyed by the feeling that Bioware was pushing the mages on me as the "obvious "choice. We get a longer and more thorough intro to the mage-issues before committing, we meet a (future) companion, Redcliffe is very close to Haven, and we're told the Venatori have it out for us personally. Lucius is obviously up to no good with the templars either, but it feels a lot more remote and isn't nearly as fleshed-out.
Still, Champions of the Just is the choice for me, and I'm glad I stuck with the plan to go for the templars on my first/canon Inquisitor. The mission itself is very good, Ser Barris is a fine side-character especially if you keep him alive, and afterwards the templars know their order is a leaderless mess that has utterly failed -- while Fiona remains a smug ******* who would do it all over again. She is the biggest reason why I simply can't stomach siding with the mages.
Also, I really like Cole, and he's so unusual that he needs the deeper introduction he gets in Champions of the Just. It makes it obvious that he's not human, but it also makes it obvious that he's on our side, helping when no one else could have. Gotta love how his interference pisses Envy off.
Also, seeing Dorian supporting Roderick till he dies shows an angle to the character that you might not otherwise expect, while Cole doing it is par on course.
My explanation for going for the templars despite the uneven setup was simple: the Inquisition doesn't have enough magical or anti-magical backup for me to happily waltz into an obvious trap set by a time-manipulating magister, especially for people as painfully selfish and stupid as Fiona and her cohorts. I intended to grab the templars first, use them to nuke the Venatori into the next age, then kick some sense into the surviving rebel mages.