The Inquisition might remain an international organization like the Grey Wardens, but expecting them to start taking over Circles, the Order, etc... is just a stretch too far
Well, the Templars are pretty much dead if you side with the Mages, they were discredited and shamed across Thedas, what little remains of their soldiers went to the Inquisition or are probably disbanded, exception aside, of course.
With Leliana is Power, the Circles cease to exist, so there is no more of that.
The only thing would be to take down the Chantry, but i guess that is too far 
I'm expecting any further story content to actually detail the downfall of the Inquisition.
They made their fortunes, fought heretics and gained political influence above their station.
Now it is time for the dream to die, to be labelled as heretical, to be hunted across a continent and to ultimately...be destroyed.
Well, that probably wont work unless your setup your game to be like that.
I mean, after the endgame the Inquisition probably has enough power to take on everyone but Orlay & the Qun (Tevinter, i am not sure).
But it would be interesting if we see them fall from grace a couple game entries in the future.
Maybe do something like "200 years after" or something like that and we see our Inquisition becoming a Opressive International Organization. 