Do you really think a place with living weapons and riches not attract the nobles? In a time of war there will be no Excuses, without the Chantry there is no way to prevent it.
If you think the system os flawless, you are very innocent.
Your arguments boil down to this :- The new system is not flawless and therefore we must implement the old system which created a "boiling pot that will inevitably burst" scenario, because "order".
Was the old system flawless ? It lead to a staggeringly high loss of life from countless Rights of Annulments, slavery in the form of individual lobotomy, being open to manipulation from the monarchy (Loghain in DAO), it lead to different circles have drastically different standards and environments to the point they might be on an alien planet, etc.
What is more, the argument you are making is that mages are weak without the Chantry protection. Really ? Have you seen what mages can do ? Have you seen how powerful mages are like when they are not under Chantry control ?
I would argue that is it the Chantry that made mages weak because they restricted mages from being able to wield weapons, learn martial combat properly, declared branches of magic such as shapeshifting magic as heretical for a long time and in general created the structure that benefits the Chantry.
I mean mages in the Circles are supposed to be scholarly, yes ? So why have we never heard of any scholarly publications on examining the historical validity of the Chant of Light ? You see in real life scholars disputing religious claims from many perspectives be it historical or scientific. Why have we not seen this in Circles of Magi ? Even if we have seen books that suggests Andraste might be a powerful mage, the book is typically banned. Furthermore, why are mages from the Circles made to do mundane tasks such as lighting the fires in the Grand Catherdal ? Why are the mages from the Circles who were allowed to learn how to fight were only allowed to do so under the Chantry ?
Fen'Harel puts it best :- "Your rigorous training lays a solid foundation, true. It also creates boundaries, limits, where none need exist."
I would argue this foundation created boundaries and censorship as well since we have not see any scholarly publications that were not pro-Chantry. I mean I am an academic in real life, a masters students and academics love to investigate controversial things and publish them in papers. Why have there not been investigation into say, relationship between Shartan and Andraste ? That would certainly make for an exciting paper. Why have most of the historical research that have been published is done by a Chantry scholar, not a Circle Mage Scholar ?
Did you not play the game ? Did you not notice how not only your advisor such as Leliana and Cullen but your companions such as Cassandra and Solas make the point that goes something along the lines of "this conflict was inevitable and was in the making for a long time..." ? Did you not see how both mages and non-mages, Andrastians and non-Andrastians seem to agree with that one point of "this crap we have now is bound to happen at some point..."
Given that this is the situation, shouldn't a new solution, a fresh solution be more useful than say, rehashing the same old system ?
I doubt that once you give mages a taste of freedom in the form of independent magi colleges, they would want to go back to the old system.