I find it difficult not to side with the mages in either 2 or Inquisition. The simple fact that the right of annulment exists shows how corrupt both the Chantry and the templars are. Sure magic has the potential to be dangerous (so does science, so should we kill all the scientists just because someone invented the nuclear bomb? No of course not.), but does that give them the right to decide who lives and dies based on what a few mages have done? The templars are a corrupt organization that has (in all 3 games) shown a desire to wipe out all mages regardless of guilt or the lack thereof. In most cases only a few templars have shown any regard to a mages life. The fact that they put any mage THEY deem a threat, regardless if that mage is a blood mage or not, through the right of tranquility (which there has been a cure for for hundreds of years but they kept quiet about), shows just exactly how much respect they have for any mage. Sure in many cases the temptation to use blood magic has overwhelmed many mages but with the continued oppression of the mages by the chantry and the templars it was only a matter of time before they broke out in rebellion. Give anyone a loaded gun and apply enough pressure and they WILL use that gun if they deem it their only way out.
As a role playing standpoint I understand that many people would not have access to some of that information, but since it's been going on for so many years I find it hard to believe that anyone who was not a self centered individual would not know SOME of the facts given the world state in DAI.
But so far through 4 completed games I have sided with the templars once and the mages 3 times. The templar story line is interesting but the mage story line is better IMHO. The decision does have an impact on the game, although somewhat less dramatic then one would think. So for me its more of a moral choice then an aesthetic one.
On the roleplaying standpoint, they can have all the facts, and react differently with that things. It all depends one the point of view, and the origin, there the people come from.
Roleplay DA:O for that. Dwarves are generally unimpressed by problems of the surface world, including templars mages, and the chantry. The see demons and darkspawn as problem, and do not care, where they come from. It matters only to get rid of them.
Townelfes react totally differnt as daylish elves. Town elfes are handled worse than slaves -- at least slaves are vealuable, and don't starve - , and believe in the maker forced by the chantry on them. For dalish elves magic is natural. And they give a **** on bloodmages or apostates. Only templars are annoying for them, because they have to keep the magic user count low in their tribes.
Qunari. They have their believe, that everyone has a place in ther order, even if that means an early grave or enslavement. 
Humans. as noble, or common folk.
Nobles believe in themselves, and ignore most other oppinions as irrelevant. Famiily is important.
Common folks try to get unharmed through life, or steal enouh to be rich someday.
From all this different viewpoints, you can make any decision, even if you know all facts, because for all of these backgrounds,different things are important goals for these people.
But if you only play yourself, with different weapons and skills, you are right. But that is not roleplaying, an these games are not made for people like that.
It's really fun to play games like Skyrim or Oblivion with your chars goals and motivation in mind. No need for the main story ever.