The save imports restricted the variety of outcomes for ending this war. Either the mages will be free canonically, or there'll be a system that will allow to show changes based on which side you supported. A Circle system that is different if you supported mages/templars/Chantry seems likely. I think the chances of very different outcomes are very low (glad to be wrong though).
Of course, they could still follow the 'the war doesn't end in this game' path, which at the moment I think it's very plausible.
Regardless, a part of the players will be disappointed.
Personally i thinking it will be limping into the next game, perhaps the one after that although i do believe the majority of the action will occur in DAI's Sequel.
Not saying we won't see a few dust ups during DAI but i have a feeling with the Veil torn asunder the Mages and Templars will at least for the moment put their war on hold to combat the end of the world; That seems like the thing Bioware would do in this situation given it allows the plot element to remain, the factions to remain and while you may impart some advantage to one faction or another that may or may not carry over to the sequel it ultimately will matter little whom the inquisitor favored.
o-o Course that doesn't mean my Inquisitor won't know what to do with rebel mages, No sir.
He knows very well what to do with them.