How to design a OS File System Hierarchy

Considerations

The file and path naming conventions will be based off the kernel you are using.
Case sensitivity of file records will also be dependent on the filesystem and the shell.

How It's done in OS

Microsoft Windows NT

System Files and System Libraries

C:/Windows/System32
C:/Windows/SysWoW64

Userspace

C:/
C:/Program Files
D:/

Program Files and External Shared Libraries

C:/Program Files
C:/Program Files (x86)

Global Program Data

C:/ProgramData

Application Shortcuts

C:/Users/User/AppData/Microsoft/Windows/Start Menu/

User Programs and Data

C:/Users/User
C:/Users/User/AppData
D:/

Program Working Directories

C:/Users/User/AppData/Temp
C:/Windows/Temp

External Mounts

E:/

Apple macOS (Darwin/XNU)

System Files

/System

System and External Shared Libraries

/System/Libraries

Program Files and Program Data

/System/Applications

User Data

/Users/User

External Mounts

/Volumes

GNU / Linux

System Files

/proc
/dev
/boot
/sys
/root

Global Program Configurations

/etc

Program Working Directories

/tmp
/run
/var

Dedicated Directories

/srv
/opt

Userspace

/usr
/home

Package Manager Installed Programs

/usr/bin
/usr/lib
/usr/libexec
/usr/include
/usr/share
/usr/src

Locally Installed Programs

/usr/local/bin
/usr/local/lib
/usr/local/libexec
/usr/local/include
/usr/local/share
/usr/local/src

Application Shortcuts

/usr/share/applications

User Data

/root
/home/user

User Installed Programs and Configuration Files

/home/user/.local/bin
/home/user/.local/lib
/home/user/.local/share/
/home/user/.config

User Application Shortcuts

/home/user/.local/share/applications

External Mounts

/mnt
/run/media

My New Ideas

1. Standardized FHS

We will consider the subdirectories (/usr/bin, etc.) and the general system directories (/dev, /proc), but we'll change the main directories (/usr, /usr/local, /home/.local, etc.) and symlink to the traditional directories.

Subdirectories:
/bin (Binaries)
/etc (Configuration Files)
/lib (Shared Libraries) > /lib32 /lib64 /sbin
/include (Static Headers)
/src (Source Files)
/libexec (Executable Library Tools)

Main directories:
/packages (System Packages)
/local (Local Packages)
/home/user/packages (Local Packages)
/nix (3rd Party Packager, Nix)
/var/flatpak (3rd Party Packager, Flatpak)

2. Modernized FHS

We'll make everything named appropriately, but without making common directories too hard to access from the command line. That is, by using CamelCase names instead of spaces.

/EFI
/System/Boot/Bootloader/
/System/Boot/Kernels/
/System/Boot/
/System/Devices/ (symlink to /dev)

[ /bin /dev /proc /sys /etc /tmp /run /var /srv /opt /mnt /root ] (Hidden in default file manager and shell, shell begins at /System or /Users/User)

/Libraries
/PackagedPrograms (subdirectories: SharedFiles, Libraries, Configurations)
/LocalPrograms
/Configurations (contains Freedesktop .desktop files)
/MountedVolumes

/Users/User
/Users/User/Programs
/Users/User/Configurations
/Users/User/[Documents Videos Pictures Downloads Music]
/Users/User/WorkingDirectory