> before we could even question if it was right or not

But we could. Early filesystems didn't have heirachy. They'd sometimes support a single level of organization by treating a prefix of the filename as directory, but nothing below that. We looked at that and considered heirarchy better.

What you lament is that we stopped with heirarchy. You wish for something more general, and that you have received. With hardlinks and ACL the filesystem is freed from its shackles of heirarchy. Most people don't need that most of the the time.

The strict heirarchy sits as the third step of a complexity ladder. The reason we stopped there, in most cases, is that it's enough complexity.