Cameron, I'm not quite sure I "get" the theme of this post, but I'll confine myself for a minute to Utopia Document. What bothers me here is the very strongly different nature of the tool. Compare this paper, for example: Ruthensteiner, B., & Hess, M. (2008). Embedding 3D models of biological specimens in PDF publications. Microscopy research and technique, 71(11), 778-86. doi: 10.1002/jemt.20618. This doesn't require a different viewer, but let's you view the models in PDF. It seems to work quite well for me.

I'm keen in principle on the idea of scientific articles migrating from PDF as default to HTML as default. In theory, with a little added RDF etc, we could do wonderful things, embedding supplementary data. However, in practice the result is pretty much rubbish even for quite ordinary articles. It seems to be very hard to get figures and tables to look right and be readable in context. And worse, there doesn't seem to be a standardised way of saving a packaged web page so that it can be left for years and then read even when the originating site has gone. Safari's .webarchive format is able to do that, but is not readable by anything else as far as I can see. the standard "save html" format seems to be a .html file and an associated directory of other stuff; hardly handy, even if in practice several browsers seem to be able to read it!