The Cerberus comparison is sort of interesting. I suppose it probably says something that on BSN, people who are Pro-Templar have a tenancy to also be strongly pro-renegade or pro-Cerberus, but I've never been one of them. I think the templars are necessarily, but I've not a Cerberus fan at all.
In Mass Effect 3, I thought there was a difference in the portrayal of Cerberus but it was not really a huge stretch of believability, to me so I had no problems with it. We always knew the Illusive Man was prone to extreme tactics. I had little trouble believing he'd make such a leap, especially since unlike the templars, Cerberus is first introduced as an enemy.
When it comes to the Mage-Templar conflict in DA 3. I expect Mages and Templars are both supposed to be reasonable equal in power and morality. Since we know templars have done bad things, the mages probably are doing bad things too, especially based on the article on the Hinterlands on the main site. I remember the old articles said that they aren't going to show them both at their worst like DA 2, but I guess that remains to be seen. I would hope we get to know good people no matter which side we choose to bring into our Inquisition. And hopefully DAI does a better job making the circumstances seem equal than DA2. I was not happy when Meredith gave me powerful reasons to side against the templars, regardless of the larger issues.
In the Dwarf Warrior demo at E-3 Mark Darrah describes templars roaming the landscape killing innocents and the Inquisitor then talks to a woman who's husband was killed by templars, but unless I misheard, Darrah also says it was "a rogue group of templars." So I kind of hope we get to see many different variants of both mages and templars, instead of just 2 or 3.
I don't know what the options are going to be for compromise, (my hopes aren't high) but apparently enough Mags and Templars disagreed with their respective rebellions that they were noteworthy enough to be mentioned in WoT.