How can I adapt my scientific writing for the modern web? Papers written for conferences and journals are today mainly available as PDFs. There are several usability issues with the PDF format, one of which is that it is not especially well suited for the modern way of reading on screens. Unlike e-book formats such as epub or mobi, it doesn't adapt to a for the user desired text size, and is especially broken for e-ink readers that cannot rely on zooming and swiftly moving around as you scan for referenced figures and tables. 

Thus, I would like to contribute to the death of the PDF to the best of my ability. All my scientific writing is already done in either Markdown or LaTeX which can then be exported using Pandoc to several different formats, but this only works as long as you don't try to use anything beyond the most basic of features in LaTeX. I guess I could in this manner upload all of my papers to a blog for general consumption, but I'm not sure this is the most appropriate way. One problem is that I won't actually use a lot of the power the web brings, e.g. direct links to cited sources, without requiring extra effort in the conversion step. 

I am sure I'm not the first one thinking about this. Are there already people doing this, and if so how? Is there an ongoing discussion about the future of academic publishing in the age of the modern web?
For journals, at least, many now publish online in HTML.  This includes many large cross-field publications including well-known venues such as Nature and PLOS ONE,
to name only a few of many.  Your paper will generally be available in PDF as well, but the default that the journal steers people to is generally HTML.

An action you might then take would be to choose to submit only to journals with HTML publication of this sort.