1) I don't like the idea or the concept that one religion is going to decide how all of humanity is going to think and act. Much less one that who's stated goal is to pretty much take over the world. "The Chant must be spread to the Four Corners of Thedas and then the Maker shall return." While it is intended to be a benign and noble goal, it's been used and abused by (wo)men to gain power. As has been proven, a central religion is not crucial to a united front. I think that the Veil tears are going to help unite the nations of Thedas. Before you say anything, even after the game I'm sure there is going to be long term effects on the Material world and the Veil.
Everyone should be free to decide what they believe in. Each nation should be able to decide for itself. Your solution is really no better than the Qun, demanding everyone be the same way.
Where has the Chantry tried to enforce a cultural monolith on everyone, though? Or even 'take over the world'?
The Chantry doesn't even rule over a nation, nor has it organized an Exalted March on expansionist principles in its entire history. The doctrine of spreading the Chant has not been implemented in anywhere near as totalitarian way as is raised here- it isn't some world domination goal.
Even in the most negative readings of history, the only point at which the Circle has organized a religious war against another religion would be the Dalish- and that's if you ignore or don't believe in any other context in the conflict.
The Chantry is a missionary religion, sure, but it has extremely little to support claims of being a 'convert or die' religion.
2) No argument here. That was one of my biggest problems with the end of Act 3 and a little fact that some of both sides choose to ignore. Look, I don't hate the Chantry, but it's time to try to severely limit their political power. They don't have to dictate over nations in order to help the poor, sick and needy. Most nations will be willing to accept their help. I see no need to demand it.
Where has the Chantry been dictating over nations, though? It doesn't determine wars, or borders, or internal politics.
The only two fields the Chantry holds authority over nations is the Chantry itself, and the Circle system and jurisdiction of mage matters. And there's nothing in particular to suggest the kingdoms feel particularly upset at the internationalization and political neutralization of mages.
3) A lot of groups oppose the Qun. While I respect your point here, that makes little difference to me. I can't throw a stone in Thedas without some group or religion taking issue with the Qunari.
But you won't find another group or religion capable of organizing and international coalition on the same scale. International unity is the key to pushing back the Qunari, and the closest international agency would be the Wardens- a very, very distant second that neither has the popular support or mandate for anything outside the Darkspawn.