A great example of a web-friendly, interactive view of a scientific paper is the eLife Lens, example here: http://lens.elifesciences.org/#00380 . They announced the open source project back in June (blog post http://www.elifesciences.org/lens/). This is the direction that web-based paper views are moving toward, and some publishers (notably PLOS) already have quite nice interactive components.
PubMed, the government-run biomedical abstract database, also recently introduced its PubReader app for reading biomedical papers (http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/). But my money's on eLife here — NCBI is better known for its databases than its user interface design (to say the least).
It would be great to see some innovation here (some publishers have absolutely awful web-based journal article views). But as the main format for paper publishing and dissemination, I think the PDF won't be going away anytime soon.