It was damage control, really. The writers did such a fantastic job of convincing DA2 players that templars were nothing but a huge bag of ducks, they might have gone a bit far in the other direction this time. There are still enough random templars (not even red templars, just random schmucks) mistaking shovels for staves and killing whoever's holding it to show the stupidity of both sides. Fiona did something colossally stupid, yes, but is her shortsightedness worse than Lord Seeker Lucius's? I'd say they're on par.
It was kinda nice to see the mage/templar conflict more as a choice between stripes or spots rather than between black and white. In DA2, I couldn't side with the templars without being filled with self-loathing. In DAI, I will probably always prefer the mages, but I have a much easier time liking my characters who go with the templars.
The mage-templar conflict was never one that could be solved by choosing a side. It's too complicated, with too much history to consider on both sides, for it to be a simple decision. One might argue that an outsider might not have any right to make a decision about it at all... but one might also argue that anyone who has a stake in the matter is already biased. Both views are right... and both views are wrong.
I like that they managed to strike a balance in the Mage-Templar Conflict's presentations. In Inquisition, both sides have equal parts sympathy, validity, weaknesses and flaws with several characters being willing to admit that both mages and templars are to blame in one degree or another.
This is a huge improvement over DA2 where the conflict was presented as too bleak and dark to bother caring. It was hard to be invested because both sides were presented as oppressive, crazy, murderous or dangerous and yet the story still forced you to pick a side as though it mattered when taking a third option would be a very valid though difficult option for Hawke in addition to just bailing.
The problem I have with Inquisition is that the Mage-Templar conflict is never directly addressed. The Player basically side-steps the dynamics of the two sides to exclusively pick one faction while leaving the other to drown in red lyrium. There was never a direct moment where the Player could directly pick a side, destroy/conquer one or both sides, or create a working truce to face the common enemy known as the Breach (giant hole in the sky) and Corypheus (1 of 7 reasons why everyone hates magic)
Otherwise, the presentation is fine and there's enough room to deal with the side that you pick in a reasonable manner. Choosing mages doesn't automatically mean that you're their best friend nor is it the same with templars.