Unix is weird because it evolved organically and without a unified direction. But it remains because power and familiarity beat user experience. Yes, the "pure" Unix tools are awful, GNU improved on their usability a lot. But they're still a simple command that does something. Except Autotools. Those should burn in eternal damnation.
Since when "evolve organically" become bad? Unix was created as a tool to solve unbounded problems. It is not possible to attempt to have a complete solution when the problems are unbounded. Today, vast computer users have bounded problems -- surfing webs, messaging, playing games. With the bounded problem, it is possible to have complete solutions -- Chromebook, iPad, etc. are for them. They are not supposed to deal with Unix just like drivers are not supposed to understand transmissions or engines. Engineers sit in between the components, tools and the products, consumers. If the average computer users have problems, blame engineers, not the tools or framework that engineers deal with. And for engineers, they still appreciate today that the underlying tools and frameworks are created versatile enough to solve unbounded problems. And for some comsumers would like to think they are smart (or cheap) and would like to bypass engineers, then they shouldn't complain or they are mixing up their problems.