Sorry, I didn't mean to propose that all of this data would be included when you download the document. A downloaded document could be as simple as a hash or a document identification # (or a magnet link :)). You open this document in a program like Papers and, after downloading the main text, presentation style sheet and main figures, could then selectively download whatever you'd like. So, if you want to zoom in on those fly eyes, you right on the image and get a context menu that allows you to see the original image.

These are implementation issues. The document format does not have to contain any supplementary or additional whatsoever. It could contain references to where the ancillary content is found. It is then up to the interpreting program to decide how it wants to allow you to download that additional content (e.g. automatically, selectively, based on heuristics, etc).

The practical upshot of this is that you get to keep all the data related to the paper in one place with one organizational tool, with relational information intact.