Personally, I like the inverse: everything is a file in Plan9/Unix/Linux world. Programming is ironically simple, and you pipe around input and output from pipes and files at the ends or in between. Trying doing the same with Windows, and it is damn near impossible to write one-liner anything unless your learn protocols like WMI and how to play with the Registry, which is not fun when querying and writing keys with simple .reg files you import and export.

What I wanted to be the future, especially after that Oberon OS article here not so long ago, is the best of both world. This paired, with better OS level analysis of files and dedup (hardware or software) is cool. I think we should just move towards the OS X model (and I am very, very anti-Mac, so you should know it must be pretty good for me to conceed any wisdom in their approaches): power users I know, including yours truly, will dump all their files in one or two places and Cmd + Space their way to search files and apps through the Sherlock utility all damn day. Now moving towards filesystems with version controlling UIs built into apps and files is a great improvment (a la the Nextstep cum Etoile Linux revolution).

Pair that with better OS level tools, and I will continue to see Unix toolchains with more refined GUIs as the answer when we move away from file and into search. That is why Gmail and other tails continue to be popular, most of us are tool lazy to organize or screw up our own organization systems, and search allows quick impromptu sort methods to help us with the basic stuff.