I read the first article, and I have to say, I did not see anything that proposed what should replace files. There was the vague "encompass metadata within a file abstraction", but really, what does that mean?
The main point of the article, as I read it, was that what a user *believes* a file is and what the storage media/application calls a file are often completely different and that the next form of "file" should better represent what a user thinks of as a file--i.e. the smallest allocatable unit of content, e.g. a photo, a contact, a spreadsheet, a document--and the actions they want to perform on it.
The article gave the example of a OneNote Notebook. On your computer it stores Sections as files and Notebooks as folders of these files. This makes sense from a technology perspective. But a user (a normal one, not a Slashdot one) expects the Notebook to be stored as a whole indivisible unit. And not every storage medium stores the Notebook the same way; SkyDrive was given as an example.
On the other hand, I don't think this is uncommon for a research paper. Not every research paper is intended to be a fascinating read about deblur technology in Photoshop. We're taught to "not point out a problem unless we have a solution", but that's not always the best philosophy. Sometimes it's perfectly valid to point out the flaws in something without knowing how to fix it; sometimes the problem is that people don't see there's a problem and the first step is jut raising awareness there's a problem.