After a little more digging, I've found that pdf files can have named destinations, like eqrefs, so you don't have to use page numbers as references. See http://www.tug.org/pipermail/pdftex/2007-October/007383.html for how to make them in LaTeX.

This does require whoever generates the pdf to include the labels, but then so does html. It shouldn't be too hard to generate a reference to any named equation in a file.

What exactly is your problem with current PDF readers? PDF.js is pretty nice for browsers, Preview.app is standard on OS X, Linux has several that were fine and I know that Windows has many that are considered good alternatives to Acrobat Reader. Even phones and tablets do a good job, though e-readers do not.