I will not answer any off-topic posts. Its really impolite to ignore the mods when they say stay on topic.
They were ruled by the Templars, who could legally do whatever they wanted except everything they couldn't and didn't do that any effective system of rulership would have allowed them to do.
Meredith couldn't even search the rooms and private property of her own tower, when she was at the height of her already highly disproportionate and barely restrained power. Even liberal democracies have governments that can do that. Meredith didn't get to dictate the promotion or alignment of mages, only performed unilateral tranquility very late on when she was blatantly breaking the laws in place, and couldn't even dictate the political leadership of the mages (which is one of the key tests for effective autonomy of a subordinate group- when they can have and keep their own leadership).
I'm quite happy to call a spade a spade, but you have to show me a spade first. Even in Kirkwall the mages had substantial autonomy, despite the abuses of Templar power and restrictions. It was certainly restrictive, but autonomy doesn't mean 'free': it always functions within the scope of what exactly is up for autonomy.
The separation from chantry is the important factor here and it was the main concern of Fiona. The circles should exist and mages must be confined but they should decide their own fate because the chantry dictates everything. For example if we are looking at things rather courteously, say mages are unhappy with a certain Templar who patrols inside the circle. The mages should have the power to replace this Templar by sending him to outside patrol and bringing in another one for the same duty. This is just a simple example and there are many more to be made. Whatever decisions mages make they will be ones affected by it. And the Templars have volunteered.
Mages are kept like living weapons who are called upon when needed, its wrong on so many levels. After the separation each circle will be like a nation and when Thedas needs help they will decide how to aid others, they will also decide how many of their brethren should join the grey wardens. This way no nation can use mages to fight other nations, because for example the circle in Orlais DOES NOT belong to Orlais, its an independent nation of mages and therefore its not obligated to aid Orlais in attacking Ferelden. Using mages in a war between nations only brings catastrophe and destruction and must be avoided at all costs.
Also the circles will not be based on bloody Gallows (just look at the name ffs) a scene that horrified every single man woman and child when they saw it. And lets be honest here, life is not fair and mages are born with extra gifts and are precious so they actually deserve better living conditions.