Also as someone who has strong opinions, I concur that PDFs are great, especially for archiving purposes. As a distillation of important information, I think they're ideal.
That said I think we need something else in addition to PDFs, rather than to replace them. Dynamic graphs, for example, and the ability to export raw data. In my field, rotatable/zoomable 3D views for molecules and crystals and the like would be great, as well as being able to measure bond lengths and angles. This would be infinitely superior to a static 2D projection. But these should all be in addition to: I still want a PDF I can take with me and read offline if necessary.
1) There's not good broad support for 3D views in PDFs; I imagine it won't work on most things other than Adobe Reader. What does it fallback on if it doesn't work? etc. And in any case, it's a corruption of what the PDF document format was "meant" to be, which is a document format guaranteed to display the same on all devices.
2) The 3D data isn't useful. It's raw information, rather than the metadata. If I'm looking at a 3D view of a crystal, I may want to export it to manipulate the structure myself or use it in my own simulations, so I want to know what atoms are there and information about boundary conditions, symmetry and the like. I specifically don't want a list of vertices and edges that, say, make up the individual spheres that represent the atoms.
That said I think we need something else in addition to PDFs, rather than to replace them. Dynamic graphs, for example, and the ability to export raw data. In my field, rotatable/zoomable 3D views for molecules and crystals and the like would be great, as well as being able to measure bond lengths and angles. This would be infinitely superior to a static 2D projection. But these should all be in addition to: I still want a PDF I can take with me and read offline if necessary.