I think the folder based, tree-like file system is common but it's not the best. Indeed i believe a good classification of a file is better than to place a file in a certain 'place' e. g. folder.
Files are different in content and so, a mp3-file contains different meta information compared to let's say a png-file. Shown in a list with columns a problem occurs, just columns like size, creation-date etc. are in common.
If you look at windows explorer for example, the columns change when certain file types are detected. If you habe lot's of mp3-files in a directory for example, columns like Album, Title etc. occur. If amongst these files there is a png-file, these columns/cells don't make sense for that particular file/row.
I have found out that many times it would make sense, to place a file into more than one folder, just because there are more than one classification properties that identify the file. But why should a 'place', a 'folder' classify a file?
If i have a car, it doesn't matter if it is in the garage, in a parking lot or elsewhere, it's not the 'place' that identifies my car, but it's properties.
When all my files are classified properly and accurate by meta-data, it doesn't mind where it is stored, it's just in some 'cloud'. If i need to obtain a certain file, this should be done by specifications of the meta-data.