I have Apple ecosystem in my home and within couple of my friends. I just love how it all works together well. Except one thing: sharing and syncing.
The document sharing between computer and ipad through iTunes->iPad->Apps->App (in second! list) is just overcomplicated and does not even allow real synchronisation. That way of sharing breaks logical document coupling as well (by-project, for example). The way of sharing documents between apps is limited as well and it forces me to have duplicates... There many other little things.
I think (and strongly hope) that this is just a transient period. Looks like Apple would like to get rid of classical file system "feel" on the user's side. They either have no human friendly solution yet (measured on Apple standards) or want to do it step-by-step, so users can accommodate to changes gradually.
iCloud is application/document type based storage, iPad is application based file storage. They even added a view to finder: "All My Files", which also hides classical file system way of browsing files.
I do not think that Apple is done with file management evolution. But I feel, that the classical hierarchical file system structure is not the way to go in the cloud based file system...Consider not only your document syncing, but also synchronized file sharing with custom categorization...