I don't care about the GUI tools, I just need an editor, a terminal and a web browser. And maybe Sequel Pro once in a blue moon. The MacOS GUI is quite annoying when you want to do stuff fast like for instance move windows between virtual desktops or switch the desktop with the mouse wheel.

The tooling is just not there (old Python, old Perl, old Ruby and of course different versions from your deployment environment), you have to resort to third party tools such as homebrew or macports, you have to install Xcode to get gcc, you need an Apple ID to do that, the system level API is incompatibile with Linux, the filesystem is or at least was case insensitive. New MacOS versions after El Capitan are also getting worse at compatiiblity with other Unix-like platfroms. It's a pain to set up a development environment really, especially if you use any dynlibs. Instead of a VM we have a staging server where we deploy and there are almost always surprises.

In Linux the tooling is just there, a few seconds and one package manager command away. If your package is not there then there are PPAs or OBS repos. You can reproduce the platform you're deploying as closely as possible and there are less surprises.