Disk space for binaries has not been a problem for decades now.
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.
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).