What autonomy and independence? The mages are essentially an amorphous group of particularly dangerous refugees. They never had autonomy - and squatting in the woods in muck while starving didn't doesn't really make them autonomous.
It does, actually. It means they can choose their leadership, their internal policies, their external relations, and so on. It's not autonomy free from outside pressure, but nothing ever is.
But, most specificlly, the autonomy and independence of a polity. As loose and disorganized as it was, the Mage Rebellion did (temporarily) assert itself free from external control. It was a mess, desperate, and doomed, but it could choose how to do such things. By taking Ferelden's sanctuary and being dependent on Ferelden's hospitality, it lost that discretion.
Not that I disagree that mages "lost" the war in the sense that they didn't really seem capable of killing all of the templars, but there was very clearly no endgame to what they were doing here. It wasn't even like a slave rebellion, where there is at least some identifiable goal and state authority against which to rebel.
Oh, I agree. The rebellion was unplanned from the start, and I've criticized this for years. I'm pretty sure there are posts on the DA2 board where I argued that the mage rebellion lacked an actual achievable goal, and I certainly did before DAI.
Which is why the Conclave works from the framework of negotiated, face-saving surrender to end the conflict. The mages don't have an endgame- but the Templars can't have one either without the Chantry's support for the Circles again. Without Chantry support, the Templars can't run new Circles.
It would be one thing if e.g. the mages just tried to clear out their Circle Towers and turn those into an independent self-governing city-state, but essentially it seems the gameplan was to go squat in the woods, so basically: "Independence Vote" => ??? => "Profit" being the gameplan here.
You forgot Fiona's favored step: "**** the Divine."
Which is why, ultimately, a Conclave is a resounding success for the mages, because it's the closest thing they can have to success: a recognition of their standing and status as a polity and a willingness on the part of the Powers That Be to address their grievances. It's not clear what, if any, concessions the Divine was prepared to make, but if they did get concessions, and if the Divine did bring the templars to heel (perhaps by forming her Inquisition and splintering their order), then ultimately their rebellion wins.
I'd argue the opposite- the fact that they are coming to the Conclave is the sign of failure, because the Mage position at the beginning of the war was 'no Chantry authority, no one else, no way.' The Mages already had the willingness of the Powers That Be to address their grievances, give concessions, and try to reign in the Templars. That's what the Chantry in Asunder was all about- and that's what Fiona threw away when she went ahead with Rebellion, because all that wasn't good enough. Any acknowledgement of the Chantry's authority was too much.
Now, two/three years later, the mages are coming back to say that what was intolerable a few years ago is now a victory, after being defeated soundly in every theater to the point that they have to hide behind someone else's walls and army? That's not a credible claim of victory. It's not the worst negotiating hand- game theory is weird like that when you have strong backers- but it's also weaker than what they had pre-rebellion. They can't plausibly threaten to rebel again, because they've lost the battlefield and if they refuse peace they can be forced out. Without Ferelden's support, they're doomed- but Ferelden's support is clearly limited, or else Ferelden would actually be fighting the Templars.
The Mages will certainly get some concessions to save face and claim it wasn't a total disaster- but the concessions they'll get are likely ones they already could have gotten. The real party that will get concessions will be the Templars, from the Chantry. The Divine has the lever of providing long-term support for the Circles... but many in the Chantry want to do that regardless, and the Templars have clearly maintained a support base separate from the Chantry that make them non-dependent on the Divine's good graces. If Justinia wants to leash the Templars... like Vivienne says, a leash can be pulled in both directions.
If Justinia could enforce a leash in the first place, there wouldn't have been a Templar revolt in the first place. The Chantry's done nothing to change that... and the only thing it can plausibly offer would be the mage's surrender. Which would be capitullation of the mage rebellion's goal, and victory for the Templars. Otherwise, the price the Templars impose for even a symbolic leashing could be a real change to who holds that leash.
We're talking about a group of imprisoned intellectuals, who had no real military training, absolutely no territory, no supply chain, no resources, and, apparently, almost no goodwill against the populace, with no political standing to speak of at the outset. That they got political standing, even by virtue of being killed brutally while confronting the templars and squating in the woods, until the ruler of Ferelden took pity on them and the Divine sided with them over the templar order (or so the templars would say) was a victory.
Nah, they never got political standing- they already had it. What they got was being forced back into the political engagement. The mage rebellion kicked off over attempted Chantry negotiations with the Circle on the topic of reforms, and the mage-hardliners refusal to settle.
The mages didn't earn a spot at the negotiating table they previously lacked- they returned to a spot they'd previously walked away from after a great many of their lot was killed. If anything, going back to the table was a cost imposed on them by Ferelden in exchange for pity and protection- 'if you don't make nice, back to the wilds and the Templars with you.'
Remember, the Mages weren't rebelling in order to negotiate reforms- the rebellion was instead of negotiations, because any Chantry and Templar involvement was too much.