I can't help but wonder how much of the kneejerk reaction is due to "cosmetic" parts of the design rather than the functional parts. For example, I notice that a lot of my initial reaction is based on the capitalization; "Programs" with a capital "P" (probably unfairly) evokes an emotional response due to reminding me of the Windows "Program Files" naming, and (perhaps slightly more fairly) I'd probably find it mildly infuriating to type "LibX11" rather than "libx11". Even though Linux filesystems are generally case insensitive, I imagine that package names would still be unique across casing, and it seems pretty likely that a Linux distribution focused on making the filesystem hierarchy more user-friendly wouldn't end up putting a second directory on the root that differs only by case. As silly as it is to verbalize, I genuinely think my initial reaction would be less strong if the naming convention examples were "/packages/libx11/1.6.9" and "/packages/gcc/9.2.0", and I don't think the benefits would be diminished at all by naming things like this.