This is direct action. It isn't script kiddies, it isn't Anonymous, it isn't a random 1337_h4xr pulling off some minor corporate sting. It's the real deal, it's programmers putting their lifeblood into an endeavor that changed the fate of nations.
So whatever flaws that happened to exist don't change the inherent absolute confidence of the maneuver, nor does it change the precision you praise in your post.
But it also means that it can't be perfect. Anything that's so grounded in reality will not be perfect. That's the rules of playing the big games--you can't please everyone, you can't perform to the theoretical maximum that the weak articles that call it "nothing special after all" espouse.
Because that theoretical maximum was out of the reach of stuxnet's writers from the beginning, and they fucking dealt with it. People writing articles now have had nothing to do with crippling Iran's nuclear capability, if even for a moment, and the hogwash in the blogosphere that exists is so much shallow posturing.
As someone who has actually read the code, my opinion is that yes it was special, but not because it was brilliant. It took a lot of resources, and although there was clearly a relatively high degree of skill involved for at least parts of it (finding 0days), there were not really any new techniques. So, I personally find it impressive because of the sheer amount of work that went into it.
I think it is more the principal of it that is noteworthy - if someone tried to make a movie plot about that a few years ago, we would have scoffed.
The reason that it was obviously a nation-state is because the number of people that worked on it, the amount of time they spent on it, and what the group would stand to gain (nothing), would not have been funded by any other entity. I won't go so far as to say it would be impossible to do by someone else, but that is improbable and really would not make much sense at all. Combine that with various external clues, and it is really obvious.
† If that's really the "target"