I think having Vivienne, Dorian, and Cullen in the party will be really interesting where the mage/templar conflict is concerned. All of them bring perspectives that haven't been deeply explored yet. Cullen has seen the worst of mages, but he's also seen the worst of templar control. Vivenne is a mage who favors control, something that not even Wynne could be described as. Dorian comes from a world ruled by mages.
If we've learned anything from DA2, it's that power corrupts. If mages and templars had more of a symbiotic relationship based on balance and mutual agreements, rather than fear and control, it would probably be better for everyone.
The thing is, and this just occurred to me, but mages and templars (outside of Tevinter) had very different kinds of power. Mages had this reality altering power - very fearsome - but lacked any political or social power. That is were the sympathy for their victimization comes from: they are essentially like political prisoners under house arrest... except they can burn people alive with their minds. On the other hand, templars have tremendous social and political power, be it with the Chantry, with how the population used to see them (according to Cullen), and with the control they wield over the lives of mages. But at the same time, individually, templars are squishy people in metal suits that would be easy to burn alive if they couldn't somehow stop mages from casting spells (or if mages used blood magic).
So it seems like the problem with the symbiotic relationship is that while there is a way to give mages social and political power (which under the old system they lacked), there is no way to give templars an equivalent to the awesome power mages wield.