Just because the war gets resolved early on won't necessarily mean that the effects of it aren't going to be felt through the rest of the game - no matter the results, this is going to have a major effect on the landscape of Thedas. Things can never go back to the way they were before, with the Circles and them being under Templar control. That's just going to put things right back where they were and spark another war again.
So I think it'll be like the first act's BIG DEAL, having two or three main quests with a handful of related sidequests, and that it's going to have a significant effect on the game itself. I'm reluctant to say it'll have severe consequences in future games, just because you can't have two wildly divergent results and expect future games to be able to account for it, so I wouldn't be surprised to see it 'smoothed out' in future games, to some stage that can feel like a natural evolution of any result. And there'll probably be a handful of proverbial fires to put out after it, because I doubt that just because the war reaches an official end means that all parties will stop fighting it.
As for how I WANT to resolve it? Trickier - I do see a need for a place like the Circle, and as well as someone non-magically inclined to remind others where the line needs to be drawn. The Chantry's system hasn't worked, but neither has the Tevinter model. And, no matter what, it's going to have a LOT of growing pains because there are scars still healing in the aftermath of the war, so tensions will still be high between mages and non. I refuse to entertain the thought of executing mages at the first sign of magical ability, so that idea's off the table as well. Giving mages their own 'territory,' so to speak, is a problematic affair, since it would require displacing people, and the elves would probably get upset at taking the time to do this for mages but not them. So I don't really see a solution that will be an immediate fix to the problem. But what's going to be most necessary is communication from both magical peoples and non to find the right solution. If the Inquisition, as led by our Inquisitor, has to take on the role of 'neutral third party' in making sure that another war doesn't spark, that the mages are treated humanely and non-magical people are protected, I'm willing to accept it, at least in the short-term.