If I try to understand the point that this guy is making I fail to see how it is better. What he and a lot of people are saying is that each application should have its own directory separated from the rest of the programs. Wrong! Again, this is thinking Windows, where indeed you install each program in a separate directory. God forbid if you put them all in one or two folders.
Important to know is that filesystems are outdated. Sure you need them, but who cares how they are organized? If I install me application through Synaptic it is added in my menu and just works automagically. Why should I care about where all the files are located, all I want to do is use that program.
What about user data? This is already taken care of in every Unix, each user has his own directory, called home to populate with anything he wants. Ubuntu takes the right approach and will try to guide the user into only his home directory with his own personal stuff in it. Browsing the whole drive is possible, but not many people will access it (this proves the point again that nobody is interested in what the OS does with programs).
How the user structures his data is unimportant. If you haven't figured it out yet, the way data is displayed to users has changed. Programs like F-Spot, Rhythmbox, Evolution and Beagle all take care of data sorting and searching for you. No longer is it necessary to create deeply nested directory structures which are mostly lagging in efficiency anyway.
Still, to provide all these features the filesystem needs to be good, stable, fast and recover easy from errors or failures. Luckily Linux already provides several of these, unlike other systems out there which require the user to spend time managing the filesystem.