I'm all for any easier file organization system as long as it's portable between systems, allows a large number of files to be locatable and usable immediately after being plugged into a system (i.e. without a lengthy indexing process), and doesn't make it difficult to share files between users in a network (e.g. a Samba set-up in an office). I don't know if there can be any such system that doesn't become as "complex" as the current folders-in-folders way of doing things. Most of the systems I've seen assume that I only access the files from this device and I'd never need to copy them to external storage or share them with another user not necessarily using the same kind of system as I do.

Maybe a hybrid system, like the one being done in GNOME, where you have the traditional underlying file system present, and a separate indexing program (GNOME documents) that enables searching by content, context, date modified, etc would be best.