The rigidity of the Qun would not be very effective, revolutionary inventions and sudden groundbreaking inspirations usually come from people that have chosen their own path and their perfect environment for their ideas.
Imagine Newton living under the Qun, maybe he would have been forced into the role of a farmer for the rest of his life. Things like that would happen all the time in the Qun, simply giving people roles after some rough evaluation of their skills doesn't work at all.
It reminds me a lot of what Javik said in ME3 regarding the Protheans, who were so rigid in how they went about running things in their Empire, the Reapers were able to blindside them as they were unable to change and adapt to the new set of circumstances they found themselves in.
In that way, I don't think they're too dissimilar from the Qunari, who are also locked into certain trains of thought that make them unable to consider any other options or course of actions aside from the one that the Qun demands them to take?
Keeping with the Mass Effect examples for a moment, could you imagine Shepard being as good a soldier if they followed their orders to the letter as the Qunari do with the Qun? Would they have still stolen the Normandy and taken it to Ilos, or would have have followed their orders blindly and remained grounded, even knowing that this would cause galactic destruction?
Or in ME2, would Shepard have joined Cerberus to stop the Collectors, even though they were flagrantly disobeying their orders and siding with the enemy? Is it better to side with Cerberus (or Tal-Vashoth) to end a problem that the Alliance (or Qunari) won't admit exists, or sit back and do nothing?
I think this is the basic flaw with the Qun. While Qunari seem to be allowed some leeway in how they interpret their role and demands of the Qun, the negatives far outweigh the positives when it comes to the basic restrictions in freedom that are placed upon them on both a personal and societal level.