The problem is that you are treating Mac OS as if it was a Linux distro. If you want the Linux experience, with package managers and command line utilities and X11, then Mac OS is not a good choice.
Package managers with automatic dependency resolution are a typical feature of a Linux installation. But they go against the core principles of Mac OS X. Software on Mac OS X is distributed as self-contained packages, that can either be simply dragged to the application folder or installed by the Mac OS Installer program (or with single click if the Software is available on the Mac App Store). Typical software written for the Mac has no external dependencies.
The fact that package managers like homebrew or MacPorts exist does not mean that they are the preferred way to install software on your Mac. Compare it to wine on Linux: You can run Windows software on Linux, but it will never be the real thing. MacOS tries to be compatible to Unix, but nothing more.
Part of the rationale for package management with dependencies in linux is so that libraries are shared (only loaded into memory once) between different executables. If OS X is giving up some of that sharing in exchange for simpler installation, I wonder how much that has to do with the memory usage complaints in the comments here.
> If OS X is giving up some of that sharing in exchange for simpler installation,
I don't really see how OS X has 'simpler' installation than any well-structured Linux distro. What could be simpler than typing pacman -S <packagename> or apt-get install <packagename>, using a single, built-in package manager that automatically fetches, builds, (possibly) compiles, and installs all dependencies at the same time?
Even if you're terrified of the command line, it's not like you can't build a GUI that makes that process look more appealing.
And please don't try and tell me that brew or macports are replacements - they're not. They're ersatz substitutes that do a passable job of installing some (but not all) development packages and basic applications. They don't manage system libraries, and they don't manage many applications that have to be installed from the App Store or from .dmg files. That's not one system - that's three or four, and they don't all play nice with each other.
In the time it took me to write this comment, I was able to upgrade all of my installed applications, system libraries, python modules, and absolutely everything else - all in one go.
Command-line or not, I can't see how one can argue OS X has 'simple' installation on any dimension, compared to (most) Linux distros.
No, I'm treating OSX as a UNIX. It is advertised as such. I know that you can use the app bundles. But they are only useful for GUI applications. I usually run applications like octave or gnuplot from the terminal or other applications (e.g., Emacs).
It doesn't matter if MacOS is advertised as UNIX or not. Technically, it is UNIX.
The practical issue is that you are using GNU programs written with the Linux/GNU operating system in mind. Of course this experience is sub-par on the Mac, because neither the Octave- nor the Gnuplot-developers see Mac OS X as their primary market.
Package managers with automatic dependency resolution are a typical feature of a Linux installation. But they go against the core principles of Mac OS X. Software on Mac OS X is distributed as self-contained packages, that can either be simply dragged to the application folder or installed by the Mac OS Installer program (or with single click if the Software is available on the Mac App Store). Typical software written for the Mac has no external dependencies.
The fact that package managers like homebrew or MacPorts exist does not mean that they are the preferred way to install software on your Mac. Compare it to wine on Linux: You can run Windows software on Linux, but it will never be the real thing. MacOS tries to be compatible to Unix, but nothing more.