Bias against the templars? Seriously? I can't see it. Of course, much of the game had some of the bigger NPCs passing the Idiot Ball around like a game of Hot Potato. No one came out of that looking good. I haven't gone Templar-side yet; I plan on it after the hotfixes for Patch 3 come out.
I can say that I also found Fiona irritating, and I haven't read The Calling yet. I was neutral about her, despite some of the complaints about her (stuff like being Alistair's mom and curing the Warden taint.) I'm not neutral anymore and as someone pointed out, she gets away scott free.
My opinion of the leaders of the Rebel Mages and the Red Templars, and about the two groups in general hasn't changed at all. They are both idiots, and with the exception of the Broken Circle quest in Origins, it always comes down to this question: "Which group is acting the least idiotic in this game?"
I've picked mages for RP reasons. My Cadash wasn't very familiar with magic (she smuggled lyrium, she didn't study about it,) so she figured that fighting magic with magic would work well. My current character is a human mage that's pro-Circle, but did take in the mages. It made sense for her. For my next planned character, my human pro-Templar/Templar character, she would see the Templars more favorably.
Still, as far as myself as a player, and as far as this game goes? Well, Fiona allows herself to believe the lies of a Teviniter magister, who one of the more obviously evil characters I've seen in awhile that was human. She does have no consequences really for her actions overall. Her getting exiled from Ferelden didn't have any weight to me as a player. If you didn't know who she was prior to this game, it wouldn't really matter if she was exiled or not. Plus, that's not a local accent obviously, so it wasn't like she was being banished from a place she really considers home.
Meanwhile, the Lord Seeker allows himself to get possessed by a demon. These are supposed to be the leaders of some of the more powerful organizations of Thedas at the moment. Fiona was a leader in her own right prior to the events of the game, and you'd figure that the Lord Seeker would have been old/smart enough to reject a demon's offer. I mean, I know he was a replacement, but he was still a senior Seeker. Oh yeah, that's real smart. 
I see the people behind those groups, the mages and templars that are just folks trying to do the best with the cards they've been dealt. Their leaders are sodding jackasses. It isn't mages or templars that I disliked siding with. It's more that I keep having to choose between leaders like Fiona or Orsino or Meredith or the Lord Seeker (didn't know about Barras until later,) which makes both groups seems like power-hungry morons.
They both need better leaders for the next game. Me, I'm glad I prefer rogues. I play other classes, but that's where my heart is.