I'm well aware that not every quest involved mages and/or templars & their conflict. I'm also well aware that there were plenty good mages, perhaps even with a single blood mage or two who weren't raving lunatics. I'm sure there were mages who just desired more freedom without the use of extreme measures, just as there were templars who didn't toe to Meredith's line.
Trouble is, all the bat-**** insane loonies on both sides got so much exposure and so little effective opposition (well, you can kill a score of them, but there's always a new one around the corner), that it simply seemed like they were all there was. They stole the picture.
There's also the problem of confirmation bias; by nature we like being confirmed in our choices. If we pick a side, we'd like them to validate the choice. However, no such thing happens in DA2. No matter how early and how thoroughly you pick a side, a horde of frothing bloodmages or zealots stand ready to throw the choice in your face. Staying neutral and mediating has the exact same result. Maybe it's because the plot is on rails to create (but not resolve) the conflict in spite of your best efforts, but the result is pretty much that I can't care for or identify with either side - yet not siding isn't even a choice...
Someone else here linked
DarknessInducedAudienceApathy, but I'll throw it in here again because it does a better job of describing what I felt towards the end of the game than I could with my own words.
If/when the conflict is revisited, I really hope we can either mediate/end it properly, avoid it, or that picking a side will actually matter and perhaps even be vindicated to some degree if we do a good job of it.