Long mage post coming up.
Personally, I think a huge part of the topic of "The Mage Problem" is always framed as two polar extremes: it's either complete freedom for mages or total restriction of mages. I think this does the reality (or fiction, in this case ;p ) of the situation a huge disservice.
We need to keep in mind that we're only ever experiencing these groups within games which tell stories...and stories revolve around conflict. Y'know what I think the average mage is actually like? Probably like that guy hiding in the cupboard while Uldred ravaged the Circle in Fereldan, or that Sweeney guy who complained about his failing eyesight. Does that mean all mages are bland? No, of course not. But we're seeing the MOST bombastic personalities because the writers aren't going to design followers that are boring. People that get things done tend to have strong personalities.
This problem is particularly present in DA2 - that game went out of its way to portray mages as lunatics bent on world domination. Despite his issues, Anders is a good example of why this doesn't necessarily apply. He was staunchly opposed to the Circle, but he was also staunchly opposed to Blood Magic and working with demons - he understood the risks all too well. In other words, not necessarily every apostate is a maleficar and not every Circle mage is free of demonic influence. Furthermore, it doesn't take blood magic to encourage a tyrannical abuse of power or great destruction (again, see Anders). DA2 skews this because almost every mage we meet is in some way corrupted, and I think that makes it seem worse than it is. I THINK Gaider has said he regretted going that far on it (no proof, but I vaguely recall this), but they needed to make the threat of magic real. Otherwise, it's just a straightforward human rights issue with no nuance to it. I think the mage-templar conflict is complicated and lacks easy answers BY DESIGN.
Similarly, judging the Dalish mages solely by the actions of Merrill, Zathrian, and Velanna is ridiculous. Those are three individuals that exist as part of a huge culture that spans an entire continent in many unconnected groups. To be sure, they all made poor decisions, but it wasn't because they were mages; it was because of their situations. Zathrian acted out of sadness and anger, Velanna the same, and Merrill obsession with the past (that's my assessment, anyway) and commitment to her people. I'm not really saying that excuses their actions, and I'm not interested in labeling them as good or bad – I'm just saying that they are probably not representative of the Dalish. I really, REALLY hope we get a Dalish mage companion that's more nuanced and less nuts than we've seen so far in a future installment.
Personally, I think the best situation would be a largely secular Circle system that gave significant control to the mages, and the Templar Order maintained its presence as both protectors (a role that the games have de-emphasized but should not be forgotten, I think) and internal police officers for mages. I say secular because the way the Chantry preaches about magic being evil is, in my opinion, directly tied to the mistreatment and abuses of the mages. One need not be an Andrastian to learn the techniques. Anyway, the Circles would serve as centers of learning and training for nascent mages as well as resources for any mage or those in need of magical aid/resources/services. They need not be framed as a prison.
But I do think it should be compulsory. Why? Because magic is very dangerous and gives lots of power to very flawed individuals, as well as opening them up to the dangers of the Fade. They NEED guidance so they can control their powers safely, I think. I would leave any culture (see: Dalish) that trains its mages in its own way out of it because the point is to make sure mages aren't ticking time bombs. Dalish with magic are paired with a Keeper to train them right away.
But aren't all mages ticking time bombs? Well...yes, in a way, but I don't think it's fair to weight that too heavily when discussing their fundamental rights. Just because a person might abuse something is no excuse for cruelty and injustice that, ultimately, make that abuse / possession even more likely. To pull from another nerdy medium, I cite Jean Grey's quote from the first X-Men movie when asked by Senator Kelly whether or not mutants were dangerous. “I'm afraid that's an unfair question, Senator Kelly. After all, the wrong person behind the wheel of a car can be dangerous.” Kelly says, “Well, we do license people to drive.” Jean responds by saying, “Yes, but not to live.”
Thus it is with mages, I think.