That's because OS X's user land is based on BSD. BSD in general is a much more well thought out UNIX-like OS than Linux. When I made the switch a couple of years back, I was surprised at how simply everything fit together compared to my experiences in the Linux space.

For desktops systems, maybe, but there's a reason almost nobody delivers SAAS stuff on Darwin, even as some do deliver on Windows.

Except for package management.

Don't agree. Self contained app bundles are great. I use homebrew for some stuff and dependencies are a PITA. E.g. multiple incompatible Python versions.