While I'm not an autotools fan by far, after reading through the linked post, I could only cover my face with my palm. There's quite a few things he lists as autotools shortcomings that's not it's own fault, but that of badly written configure.ac or Makefile.ams.

Basically, at least half of the problems he lists, is due to badly written configure.ac/Makefile.am, and not an issue with autotools themselves. Cmake lets one do stupid things aswell - it is no better in that regard.

Not to mention that some of the suggestions are downright unportable to non-GNU systems.