Concerning user interface, I think the ordinary user interface of such a system would have to be application based. Rather than increasingly impure desktop metaphor, you simply list the applications available to user. They open the application and select from the available documents. You would have some kind of list of filters, including automatically maintained filters (like "time last opened") and manually maintained tags.

You could probably have a power users interface that is "the file manager". But it's just the normal file picker, without a default filter of "files i know how to open".

But you still have a problem when you export a file. How do you export that compressed audio stream when you want to send it to your friend? You need to identify all the metadata and reconstruct an MP3 file. Presumably you could implement version 0 of this without changing the file storage, since file importer/exporter is kinda crucial. So you just cache the important data somewhere.

It would all be more important if files were still as relevant as they used to be. I used to have ogg vorbis files and photos and everything. Nowadays, it's really only code and occasionally a document. Otherwise I'm in my web browser or on an app on my phone.