Right to marry and have children, for one. Many in Thedas are limited by circumstance, but they aren't denied that. The right to have relationships for another. Wynne tells Alistair that mages are discouraged from having relationships with each other. And I think the devs said that depending on who the Knight Commander is, some outright forbid mages from having any relations at all.
The right to serve in the army would be another example. Anyone can join outside a Circle. The farmer's son, the merchant, the illegitimate noble's child, they can choose to join. Or they can try to apprentice in a craft or a trade.
Mages have none of these options. It's "go to the circle at the age of four-six, possibly torn from your family in chains, possibly abandoned by your parents who hate your existence because of your magic, study for a few years, take a potentially lethal test with the details kept from you, and then spend a few more years hanging out in said tower, hoping the templars are led by an understanding Knight-Commander, before taking on an apprentice themselves, if they don't get killed in an annulment first."
They are forced to stay in a tower for decades and are not given any options on what to do with themselves.
Anders seems to imply it's a much more socially liberated culture, what with his "robes" comment. They also do have the rights to relationships; discouraged is not equal to banned and Wynne's lover was a templar, no? I'll take your word for that last statement, but I agree that they should have that right.
They're also immune to conscription outside of the Grey Wardens, which is a very important point. Anyone outside the Circle can be forced into one; take the widowed father, a farmer at Redcliffe, conscripted into an army serving a Lord whose son murdered his wife. I also disagree with your statement about crafting; in Awakening is any indication, they are more than welcome to take up a trade; one Mage was very much into (what was essentially) botany and even allowed outside the Circle without an escort. Granted, that isn't the same as, say, blacksmithing or leather tanning, but that could be simply the lack of availability; I don't recall seeing a forge at the Circle.
You missed a bit there, but point is taken. And Annulments are rare; there were, what, a total of 17 total over 1000 years in over 10 different circles?
Except when they are (Wynne, Cera, Finn, Ines).