I think there's a bit of a disconnect between how people talk about/defend the unix shell and the reason it's actually still there. People often defend the simplicity or philosophy - despite, as the article points out very well, much of it being clearly poorly designed.
But really the reason most of it exists unchanged is simply path-dependancy - we used it then so we use it now. It works well enough that there's not enough incentive to drive a large change. There are dozens of different shell-like environments and scripting languages, but they never really took over out of plain intertia. That, and the conservative attitudes of people defending their Unix traditions (related in no small part to how much effort they put into learning the thing in the first place). For new people arriving on the scene, its still less effort to learn things, even when they get truely arcane, than to use something which relatively few other people use or even roll your own alternative...
But really the reason most of it exists unchanged is simply path-dependancy - we used it then so we use it now. It works well enough that there's not enough incentive to drive a large change. There are dozens of different shell-like environments and scripting languages, but they never really took over out of plain intertia. That, and the conservative attitudes of people defending their Unix traditions (related in no small part to how much effort they put into learning the thing in the first place). For new people arriving on the scene, its still less effort to learn things, even when they get truely arcane, than to use something which relatively few other people use or even roll your own alternative...