I couldn't get past this part:

    Even geeks can’t handle folders in folders

Hierarchical file systems weren't invented because it was ancient times and they were the easiest thing to produce. Hierarchical file systems were invented because they are a really, really good paradigm for storing and retrieving hierarchical data - which I strongly believe is still the case for the majority of files.

I didn't read further in to the article so perhaps I missed where this same idea was discussed, but I think a useful idea going forward would be meta-tagging of data. Something very basic like the ability to flag a file and later search or sort by those flags. Do it for specific folders, like the Documents folders. Done.

Now the 'non-geek's can deal with flat file structures and us 'geek's can do smarter things.