It could be deliberate
I can think of at least two reasons why the creators of Stuxnet did not bother with more obfuscation etc.
1) They wanted it to be found because they expected that the Iranians would then form a circular firing squad and/or demoralizing witch hunt. Either of which would drastically hinder the recovery from the outbreak. There is evidence that, combined with a couple of assassinations this has indeed been the case
2) It is misdirection because there is also Stuxnet2 which has not been found and which continues to wreak havoc but that havoc is believed to be caused by Stuxnet. Thus the recovery is hindered because such computer techs as the Iranian nuclear industry has waste their time hunting for the original Stuxnet instead of looking for Stuxnet2
I've got no idea whether either of these reasons are valid but both seem quite plausible, and in the process of thinking through the arguments for those two I've come up with some others. Now I don't say these reasons are correct but I do think the argument isn't as clear cut as the original article suggests.