I am very tempted to try to write my next publication in HTML. However, I seriously worry about things like footnotes, code examples, floating figures and refer

I am very tempted to try to write my next publication in HTML. However, I seriously worry about things like footnotes, code examples, floating figures and references. CSS3 seems to have support for many of these, but I wonder how well the convert-to-PDF pipeline really works, and how flexible it really is. It's bad enough if I have to convert my original source to some other format years down the line, but it is absolutely critical that I can at least create the initial PDF correctly.