It's bad either way. There's no perfect Divine, there's no full stability in Orlais, and everything the epilogue mentions with the mages and the templars seems shaky and temporary. And once the game is over, you're no longer in control - essentially the Inquisition is a huge NPC that can turn out any way the developers want this NPC to turn out. And there's absolutely no indication the Inquisition is going to play nice - see the endings for Cullen(army keeps everyone in fear) and Leliana(through secrets and blackmail you're in control) and Jo(power to shake kingdoms). It's really, really, really a cause for concern either way.
All of this sounds like just human nature to me, which is to say; it's complex, and that there is no 'perfect' answers. To me, this is a good thing. I don't think it should be as easy as managing to sort out peace out of something like the 3-400 years of conflict such as the Quarian-Geth conflict in two short sentences. There *should* be rammifications for the Inquisition. Like I said, I think this was the entire point.
While the Inquisition may indeed have too much power, at the end of the day perhaps what they can accomplish can be of anything greater than what's come before.