Disk space was not really the issue. Back in the day extra partitions would actually mean you waste space. It's more efficient to put them on one partition.
The issue is organisation. There is already so much junk in the bin folders. I think it would be much neater to further split the bins into various categories: "shell tools" like ls, [, echo; "applications" like firefox, inkscape, "helpers" like gnome-settings-daemon, ... There is no need to show weird daemons when pressing TAB in bash, and there is no need to show `ls` when picking an application via a GUI.
The problem with that suggestion is that some things belong in more than one category.
A much more flexible way of organizing is to use tags. This way a file could have more than one tag.
Having a tag hierarchy would be even better, so you can browse down the hierarchy as you'd traverse the tree structure of a typical file system (with the added advantage of allowing a single file to have multiple categories that it could be in).
The issue is organisation. There is already so much junk in the bin folders. I think it would be much neater to further split the bins into various categories: "shell tools" like ls, [, echo; "applications" like firefox, inkscape, "helpers" like gnome-settings-daemon, ... There is no need to show weird daemons when pressing TAB in bash, and there is no need to show `ls` when picking an application via a GUI.