most passionate partisans will admit that its filesystem, which stashes vital files in a variety of arcane directories, can be baffling to users.
Isn't that [directories] what filesystems are to provide, so things can be well organized ?
Calling them, current UNIX/Linux filesystem hierarcy, "arcane", baffles me. Unless you're Poettering, of course. There is a good reason for things to be where they are, and, due to recent increase of embedded systems, a much more valid reason to split different levels of files across different filesystem hierarchies (read /bin vs. /usr/bin).
I can accept complains about "/opt" and "/usr/local" - they might not make much sense nowadays, but if you happen to need to bootstrap from a read-only 8Mb flash device, and need to have a somehow working system before you access some external data,
you have a huge shared filesystem where a few servers rely upon, and you don't want to replicate all system files,
then I see no reason at all to change this.
Actually, perhaps increasing the diversity of directories might come in handy (like in /usr/i686/lib + /usr/x86-64/lib + whatever you might need, and with eventual optimizations, and with eventual debug).
Or is this discussion only about directories which reside on the root of the filesystem ?