Oy, so much misunderstanding in here, must correct.
The Qunari society is in no way presented as perfect, it represents the sacrifice of free will in order to attain a perfectly functional economy. That in many peoples eyes is the opposite of perfect.
Their biggest advantage is their work ethic which you can argue is near perfect, but as a society, it is not perfect in any way. Their policy with mages and those who dont follow the qun are just two major examples. If it were a utopia, wouldnt people be flocking to join them?
You don't sacrifice free will, you accept your place in life or you don't. While I know this doesn't gel with our cultural understanding of free will, to them it makes perfect sense. Interpreting our society through a Qunari lens, someone who was raised in a working-class family and thus had aptitude for working-class jobs, but decided to become a scholar is not accepting their place in life. They're making the choice. It's the wrong choice, but they're still making it. The dichotomy of accepting a successful path or rejecting it for an unsuccessful one is not imposed by them or the Qun, it is simply the nature of reality. Having institutions which compel individuals to accept successful paths is simply helping them to better themselves, like when high school counselors try to help you pick a career. Obviously Qunari society is more restrictive, but they see allowing a farmer to be a soldier the same way we would see encouraging someone who has trouble doing basic math to be an accountant.
I don't know that their work ethic is perfect so much as every follower of the Qun accepts their task and their place in life. You can still be a bad craftsman in Qunari society, you just can't change professions if you don't think it's your cup of tea. The main benefit of the Qun is that it gives order and structure, whereas in Kirkwall everyone just tries to make money any way they can, by hook or crook.
Also, people did seem to be flocking to them in northern Rivain. The locals there still follow the Qun even though the main Qunari body has left.
So much about the Qunari annoys me, but I think they're portrayed as flawed. Sometimes I was a little disappointed with some protagonist dialogue options in conversations with Sten, the Arishok, and especially that tool Saemus, but whatever. I do wish my character could spend 100% of their time spewing fanatical anti-communist froth, but I understand that's not completely realistic or practical.
I expect the Inquisitor will be able to oppose them on grounds on other than that they're heathens, since the Inquisitor can be Dalish, vashoth, or dwarven - not necessarily Andrastian by default.
The Qunari's communism doesn't really come up much in the games, at least not from what I remember. I actually had to look up how their economy worked on the wiki. At any rate, most of what Sten and the Arishok say isn't outright communist. Communist would refer to their distribution of goods, not their caste system or their social stratification. Yes, they have a communal society, but you can have a communally-minded society without being communist. In fact, the Qun is largely based on Japanese Shinto and Bushido, and Japanese society is generally regarded as communal even though they practice free market economics.
In Origins you could very clearly point out the flaws of the Qun in your dialogue with Sten. Sten's only response is 'that's the way it is', which is more in line with circular reasoning than actual logic (meaning he can't really defend what he believes other than the fact that he believes it).
I think DA2 speaks for itself in the way Ketojan was treated and the fact that they looked to make war (manipulating/corrupting Seamus, taking in elven defectors). I wouldn't be surprised if they supplied the elven fanatic with saar-qamek only to make it look like it was stolen to appease Hawke and the rest.
To a Qunari, people like Hawke and the Warden insisting that allowing people to choose different professions because it is intrinsically better is responding with "that's the way it is."
"Sorry I'm still lost at the deny an die part..." - Sarcastic Hawke
I admire their sense of honor and duty, but a I take issues with their fatalism, lack of individuality and need to convert everyone.
And they have a problem with Thedas' rampant individuality. As for the need to convert everyone, they seem to have stopped the war with Thedas in part because of the civilians lives that were being lost. The Arishok confirms this when he says the treaty was a formality he honors for now.
I think the writer's definitely want the Qunari to be complex. and interesting. But I never for once saw them as being protrayed as perfect. Far from it. They're supposed to be aliens, weird foreigners from mysterious lands across the see. Islam to Thedas's Christendom (in the Middle Ages sense, The Qun and Islam don't resemble each other).
As an aside: Anyone else planning to play a reaaaaally Anti-Qun Vashoth in one of their play-throughs?
Actually, when the Ottomans and Catholics were waging crusades across the middle east Byzantine citizens who came under occupation actually had more in common with Muslims than with Catholics. There's far more of an East/West divide than there is a Muslim/Christian one. But yes, eastern culture does seem strange to the point of being incomprehensible at times to westerners, and I think BW captured that well with the Qunari. I think a lot of people are having a hard time appreciating that the Qunari just have a radically different culture than the rest of Thedas (read: our own culture).
I just get tired of each and every one of them refuting any possible argument for Thedosian society with what essentially equates to a "lol nope". I get why most of them do respond that way, but it's still terribly frustrating when some of the prominent qunari we meet take every opportunity to point out how everything about the rest of Thedas is wrong.
Don't Hawke and the Warden do the same thing?
Try telling that to the Qunari and their "everyone else is living wrong, so we'll force them to live like us or die" 
Like I said before, they seem to have stopped their invasion specifically because it was costing Theodosian lives. Yes, they want to convert all of Thedas, but they don't want the choice to be that or die. They want to hold off the militants while allowing as many as possible to be converted. As people pointed out numerous times in DA2, if the Arishok wanted to invade he would just do it. He didn't invade at first because he wanted to convert as many as possible, and when they threatened his converts then he invaded. Their goal is betterment of everyone (even if the Qun doesn't necessarily lead to betterment, they see it that way), which is hard to achieve when everyone is dead. It's their duty to fight and take losses in order to get more converts. I suspect that if they wanted to wipe every non-Qunari off the face of the earth they could have done so, or at least made one hell of an attempt.