If Apple had wanted to set up iCloud like that, I think they would have done so at launch. App-per-app documents isn’t a technical problem; it was a design choice. A shared folder structure isn’t “futuristic” or “hard”. There is already a ‘typical’ filesystem underneath iOS, it is just hidden from normal users.
For better or for worse, Apple decided that this is how documents should be managed in an modern OS. In fact, they decided it before iCloud even existed, with the debut of the original iPad.
Apple has clearly chosen this model of file management and, unfortunately, I don’t expect them to change their vision in the near term.