I haven't read every page, and I'm not a big fan of the Chantry in general, but here's how I see it.
There are those in the Chantry who do good. They go out of their way to try and help others. But the Chantry as a whole does have racist attitudes and tendencies. I think Gaider or Laidlaw talked about how the Chantry simply will not publicly acknowledge the elves as being equal in the sight of the Maker as humans, and by its very implication of that statement, simply see elves as inferior to humans.
It was the Chantry that declared that all elves had to live in alienages.
The Qunari may be far more ruthless, but they have something that the Chantry does not. Fair treatment of all races. And by that, I mean that if you convert, they will not treat you differently based on your race. You won't be forced to live in an alienage, you won't have to worry about racism. What you do have to worry about is fulfilling your role in the Qun. And they give you your role based on your merit and not your race. Unless you're a mage. They also squash personal freedom, tell you what you will be doing for the rest of your life, and either forcibly convert you or put you to death. If you are a mage they cut out your tongue and bind you.
Another thing that the Chantry does that really aggravates me is their favoritism of Orlais. They were founded by Drakon I and helped him build the nation of Orlais through a series of Exalted Marches. They side with Orlais in every major conflict, and many minor ones. Heck, the Divine tried to order her Templars to interfere with Kirkwall's trade because the Viscount at the time was raising tariffs on Orlesian goods. This had nothing to do with the Chantry and everything to do with Orlesian interests. There isn't anything to deny here, but what exactly is wrong with the chantry looking out for its best interests? They are based in Orlais, Drakon was very influential in helping to build the chantry up, it is there power base, what exactly is the problem here? It would be like expecting the Church of England to side with France against England. As for the exalted marches we have 1. Against the dales that was called after the dalish sacked Val Royeux, the seat of the chantry. 2. Against Starkhaven, is debatable. We really don't know the entirety of why an exalted march was called. It is the one that most fits with your belief, but it isn't like Orlais ruled starkhaven, all information says that Starkhaven was made independent. 3. Imperial Chantry-this is entirely a religious matter. Right or wrong the chantry of the imperium had broken away and the Orlesian Chantry was trying to return them to their control as opposed to their percieved blasphemy. They Qunari-again religious survival. The Qun has no room for the chantry and vice versa.
Also, in the Stolen Throne, we see that the Chantry was aiding Orlais and even endorsed to a certain degree the abuses the Fereldens were feeling at the hands of Mehren and the Chevalier's. They only changed their tune when it became obvious that Ferelden could win the war and they tried saving their butts because they were very close to being kicked out of Ferelden entirely. They supported the legitimate government of the area. Orlais had conquered Ferelden. The war was over. You had a rebel group, but that is hardly a legitimate government. You also had chantry priests who served in the rebellion, Mother Ailis.
Also, another thing that the Chantry does that really annoys me, is its hypocrisy at an institutional level. They preach that the Maker will return if the Chant is sung from all corners of the world. Leliana and Wynne discuss how the Chantry believes the Chant must be sung correctly, and that's why the brothers and sisters were annoyed if Leliana got some of the words wrong. But by the same measure, they have absolutely no problem removing stanzas or canticles from the Chant of Light when they become politically inconvenient or preach something they don't believe. They won the war against the Dales (since Orlais clearly didn't,) declared elven religious beliefs to be heresy and ordered elves to live among humans and in slums, and then they removed the Canticle of Shartan, adding it to the Dissonent Verses. The Canticle of Maferath is also in the Dissonent Verses, as we see in Awakening. To the victor go the spoils.
They also condemn blood magic by mages but condone their templars using it. That's what a phylactery is. Blood magic, in and of itself, is nothing more than using blood to power a spell or as a component within it. How exactly phylacteries work I have no clue, but I also don't consider the on the same plane as blood magic. Phylacteries are inert and don't actually affect anyone, they just allow you to be tracked.
If the Chantry truly believed that the Chant must be sung from all corners of the world and must be sung correctly, the Dissonent Verses make it impossible for them to do so since they don't sing them or believe in them because those verses challenge their beliefs or show their hypocrisy. Well, a divine is divine representation of Andraste on earth, so therefore if they choose to remove verses from the chant they are acting in the will of Andraste and know better then us mere mortals.
They claim to be a religion for all, but it seems to be a religion that favors humans, and Orlesian humans above other humans at that. Add in the hypocrisy and constant need to help Orlais when Orlais has problems in the world and they look less like a religion and more like an Orlesian front of a religion. Already addressed the orlais part. I would agree that the Chantry sees non humans as being further removed from the maker, but they are open to all races. We know there are elven templars and mothers according to gaider, they just aren't common, and city elves are mostly chantry as well, so it isn't like they are barred.
Again, there are those who seek to do good within the Chantry, but I find that at an institutional level that they are hypocritical bigots with no tolerance for those believe differently than they.
That is my impression of the Chantry. I won't really argue this, but as I have said previously, all institutions have this same fault and failing. Seriously from the Qunari to the Imperium to Ferelden to wherever and whatever races you wish to consider. They all suffer from the same. It is no more hypocritical then to hold up the Dalish or the Dwarves or the Qunari as superior to the Chantry when they all have their faliings and hypocrisies. Is the Chantry perfect, no, but it isn't the root of all evil in Thedas either. I hope that DAI shows more of the failings and problems of other cultures and groups.