Most people want a self-contained document format in order to read and share content rather than to write or modify it. That's why people have most of their music in mp3 format rather than as a collection of multitrack clips and mixdown parameters, why most people swap pictures as jgg files rather than as photoshop documents or a collection of TIFF and LUT files, and why most people watch movies on DVD or in some single-file digital format instead of as a collection of film clips that need to be rendered overnight before watching, and why most people like printed books or single-file ebooks instead of printer's galleys and versioned markup documents. Indeed, this is why most people like sitting at a table in a restaurant instead of going into the kitchen and making the meal themselves.
Look, I write and create multimedia content, I like powerful composition and editing tools. But managing all the structural information and assets for a large compound document or media project is a lot of work, the kind of work for which I prefer to be paid or rewarded in kind. When I'm just consuming and sharing the work of others, then I don't want to do all that work and I prefer a nice self-contained package that doesn't impose any administrative overhead. When it's as easy to store or share a HTML+CSS+JS document, online or off, and have it appear exactly the same way in a completely device-independent manner or even as the output of a printer, then I'll sing its praises. What I do not want is a bunch of extra files to keep track of for a single document that I just wish to add to my library and might not open again for a year. I am often much more interested in the content of a document than in the ability to edit, deconstruct, or radically reformat it.
When I was younger, I cared more about having control over things like typesetting, page flow, and other design issues, and also cared more about everything being as editable as possible. Now that I'm older I'm far more concerned with what a document is about than with how it looks. So I tend to open Picasa ten times for every time I launch Photoshop or my Camera RAW editing software, and I tend to read PDFs in the browser or in Acrobat reader far more often than I run up the full Acrobat environment to make a PDF file.
I suggest that you focus less on how you would do things differently if you were Stephen Wolfram, and more on whether his CDF format might open up some new economic opportunities, the way that PDF files have leveraged simplicity into ubiquity.