The tipping point for me with the mages is there are children in their ranks. If I could have gutted Fiona (she's the Inquisition version of Isolde as far as I'm concerned) I'd have done so. When Alexius is talking about how he will make use of the mages he's enslaved, he says something about them being used in Tevinter's wars and Fiona's aghast saying "there are children among us". She's guilty of doing crap on the spur of the moment and not making long range plans (that's how this whole mess began in the first place).
She may be competent as a mage, but as a leader she sucks ass majorly. Her only real claim to fame is she was a former Grey Warden and secretly Alistair's mother. The latter is all but confirmed when she asks if you spoke to the man and 'did he seem happy?' Yea, dumba$$ he was overjoyed you got his uncle kicked out of his home and placed a hostile foreign power on Ferelden soil... 
I hate that stupid character even more than I do Isolde, and that's saying a lot because the only person in the franchise I hate more than Isolde was Rendon Howe.