I think the bigges criticism against the Chantry is that it is too mixed up with secular power - both White and Black Chantries. So it tends to overlook the excesses of those in power and the expense of those it is meant to protect. The reason for this is obvious if you look at what happened to the Chantry in Orzammar - there it is in direct conflict with the established society and the powerful elite and before long gets eradicated. The relationship between the Chantry and ruling nobles in all countries is a bit too cosy.
I happen to agree with this. The Chantry, supported by the conquering emperor of Orlais, has never gone into a country without war from Orlais supporting it, or them supporting Orlais, and they have never actually been in a situation where they aren't in bed with the nobles.
If the Chantry followed the code of its own Chant of Light without fear or favour, I am sure no one would have a problem with it. However, when mages are being victimised and ill treated, when elves are being victimised and ill treated, it simply turns a blind eye - all are the makers children. Individual Andrastrians who correctly follow the code are people to be respected.
Again, I agree. The Chantry leaders often seem to forget why they are viewed as holy leaders by the common people.
If the Templars stuck to their remit of tracking mages outside the Circle and dealing with abominations and blood mages when they can be identified, it would not be a problem. Again, if they are chosen for their piety then that ought to extend to following the Chant of Light but clearly it does not. It is abuse of the power they have over the Circle mages that is so objectionable. Also the way they treat the relatives of mages, particularly if they are poor. It is also noticeable that when a nobleman sends a complaint to Meredith about invasion of privacy (in spite of the fact that one of her own Templars is suspicious of the man and has evidence of blood rituals) or a nobleman sends a letter begging mercy for his mage son, she ignores her own policy.
Again, I agree. I mean seriously, a woman gives her mage relative a place to sleep and some food and suddenly templars are ordered to murder her because of it? Not exactly what the Chant of Light teaches at its principles. I would also add it would help if the Chantry did NOT remove anything from the chant, like the bit on Shartan or Maferath.
My honest opinion is they removed the bit on Shartan because they wanted to feel superior to the elves and give themselves and excuse to feel good about conquering the Dales. As for Maferath's section we can find on Awakening, it reveals that Maferath's betrayal was blessed by the Maker and he was forgiven. But the Chantry teaches that Maferath made the Maker leave them a second time. If he were honestly forgiven, that would fall more in line of Leliana's views that she gives us in Origins and less with what the Chantry teaches.