I originally went into more depth, but replaced it with a small summary of my motivations. The article is more about making a distro than about agunix itself. See the website for some information about agunix.

Service, configuration and package management are not solved problems in any distro. It's only normal to list systemd and apt as cons.

apt has significant limitations vs. a more flexible package manager. I would never use an apt-based distribution; I would use a Paludis-based distribution: see its feature list for many of the reasons why.

Bloat is a concern because I don't want unnecessary system processes running, nor do I want cruft installed that can be done without. Gentoo is good at minimizing cruft, and others in the same spirit as well.

Can't help you with systemd and GNU, as I am comfortable with both.

The writer seems more like a Gentoo or Exherbo or Arch user than any of the more popular distros. In other words, one of the people who used to use Linux when it wasn't as mainstream.

They're mostly matters of personal preference or opinion rather than real issues.