What is this article trying to say, exactly?
None of the criticism voiced here is specific to Linux or the GPL. And, one, alleged, autoconf mess does not a general indictment make.
What I read here instead is a broad indictment of open source. Not entirely unwarranted in some cases, but way too broad and not argued well.
Can open source programs be a mess? Yes. So can closed source programs. The first step in doing anything with an open source anything is 1. check when was the last time the program was updated. 2. check the open bugs. 3. if you are a dev and planning to use the libraries, take a look at the code.
I know step 3 got me to junk a once-favored Python alternative to Django - code was an incredibly ugly mess of nested IFs that would discredit any programmer. Not clever - I have a hard time grokking Django's internals because it is too clever for me - just ugly.
None of the 3 vetting criteria above can be applied as efficiently with closed source, since even bug counts are generally kept under wrap.
Second, there could be case made that the BSD family of Unixes are kept on a tighter leash than Linux. But that this more due to the smaller teams and reluctance to change things much than to a GPL vs. BSD license argument. Stability over features and innovation. That's a different question, but not what the article covers.
Third, can open source programs be less than innovative? Yes, many are. So are most commercial programs. Can they be useless forks or vanity projects? Yes, and it behooves you to estimate long term viability before coupling your code or business processes to an open source project.
Last, spot the reasoning:
a) autoconf is a mess and uses GPL
b) Linux uses GPL
c) Therefore Linux is a mess
I prefer BSD over GPL in general, but I find this character assassination less than convincing. And, microkernel vs. monolithic has, again, little to do with the GPL. It's not like microkernels are broadly used in any license family.