Hi,
I think it would be really helpful to have an alternative to the default filesystem for large sites or sites that are hosted on distributed servers where the files can be saved externally to the likes of Amazon S3 instead of the '/assets/files/' folder, especially considering that filesystem on servers have a limit of either 32k or 64k for folders/sub-folders.
This can be possibly achieved by creating a custom FieldType or a Module that can hook into the fileupload process, but having this built into the core would be a dream!