In general, the games heavily leaned in favor to the mages. For starters, the support mage ending was clearly the good choice while the templar ending was the bad choice. For starters, the mage ending simply says that all abominations and demons were eventually cleared out and life went back to normal. If you sided with the templars, the ending goes how the circle became haunted, the townsfolk hated mages more, and Greagoir died and was replaced by Cullen who became a tyrant (I know it was retconned but still). Don't forget how fully supporting the Templars meant you lost your only other mage companion which potentially leaves you with Morrigan as your only mage.
Also, in DA2, Meredith is very clearly meant to be an antagonist by the end. She has no problem allowing templars to abuse and rape whatever mages they want, she lobotomizes people for the most inane reasons, and she sents death squads to kill anyone who was even remotely involved with mages. Don't forget how she plans to execute an entire circle for a crime they didn't even commit. Heck, if Anders stays with you and you side with the Templars, she's more focused on annuling the Gallows than actually punishing the person who destroyed the Chantry who is standing right there. Also, the story makes more sense for a Hawke who sided with the mages. Hawke is either an apostate or was the sibling of an apostate which makes being pro-templar quite strange since Act 1 is about ensuring the templars can't get you and being pro-templar is very strange when you spent your entire life trying to avoid them with no indication that you opposed this (take Anders' banter about the children of mages being taken away from them in Circles in MOTA. No Hawke, regardless of how pro-mage or templar you are says anything positive about this.) Plus, Hawke disappearing and Cassandra being accusatory of Hawke makes more sense if Hawke ran away after helping the mages rather than a Hawke who sided with the templars trying to keep order and stayed as Viscount.
Also, in Asunder, Lambert is very clearly intended to be a villain. Despite his viewpoints, Rhys and Evangeline who oppose him are way more sympathetic and show that the mage supporters are in the right against the dictatorial Lambert. It should be telling that there is literally nothing positive said about Lambert in Inquisition and Cole's banter even reveals he was more of a douchebag than previously believed. The closest thing that is said about him positively is Cass remarking that he shouldn't have been killed as it made the mage-templar war worse but even then Cass recants this and admits Lambert deserved to die.
Inquisition having the most pro-mage ending where you ally with the mages and have Leliana as Divine clearly shows that being pro-mage is considered a good thing. Why else would the devs include that ending with no negative consequences.
Origins made the mages look like the good guys. I always supported the mages in Origins, but those mages didn't want to leave the circle, but fix the problems that was going on. They wanted to rebuild the circle because it was their home, not because they were prisoners there. Pro-Mages always want to speak for all of the mages, but not all of them want to leave the circle. The pro-mages are just as bad as the templars, because they're trying to force something on the pro-circle mages.
Meredith was the main antagonist in Dragon Age 2, there is not doubting that. But, there were so many blood mages running around killing innocents in Kirkwall that they aren't painted in a good light, either. The story makes just as sense to side with the templars. Hawke's mother was killed by a blood mage, and he could resent all mages for that or even think that they should be in circle, so things won't get out of hand again.
A blood mage started the events of Asunder.
The game isn't even finish, so don't say any negative consequences, yet.