I agree. However, with Craig F. running the show at Apple, I bet in time they will revert back to the correct way of accessing files (not iOS' app-based approach). With Apple's App-Based approach, you will never be able to have a bird's eye view of your project. It is an organizational mess.
On my Mac, I found a song I was working on years ago along with its lyrics in a Word file & a PDF of the music sheet. It was all in a single Folder under "Composition 2007-B". There is no way in Hell I would have found all those supporting documents for that song had it been done on an iPad.
Here's how Apple could easily improve this & keep the simplicity: Allow Folders (like the Mac). Also, when you launch an App (say Garageband), it will show all your Garageband files, regardless of which folders they are in.