The whole filesystem layout is pretty poor, with massive amounts of inconsistencies (/bin, /sbin, /usr/bin, /usr/local/bin, /usr/local/sbin) between different software and even distributions. So you just wind up with everything scattered all over the place, and package managers exist essentially to corral the mess.
Everyone loves to talk about how UNIX is simple, and how UNIX concepts date back to at least the 1970s, and while that is true in theory, in practice the inconsistent behaviour and lack of much evolution has ultimately meant that UNIX's simplicity doesn't scale very well as the systems become more complex with more moving pieces.
But nobody is willing to touch or even criticise the mess that is modern UNIX because they know they will get massively criticised by the old guard and the die hards (see systemd, which is trying to evolve classic UNIX concepts and getting massively attacked, even death threats as a result).
Windows' file system is also a mess. But at least Microsoft are trying something with Windows RT "Apps," at least they're trying to move forward and progress. The UNIX world is in cryogenic suspension, even Apple has only hidden a lot of the mess and not really fixed much of it.