Is http://arxiv.org/pdf/hep-th/9907164v2.pdf#page=30 a reasonable approximation? It works in Chrome and should work with the Adobe plugin, but doesn't work in Safari. I don't know if PDF has finer scale references than page.
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.
https://github.com/amkhlv/pdfviewer
I started that fork because I could not find a viewer which would keep vertical position, and jump back after following an internal link, and have bookmarks with charhints.
There is a conceptual problem, however: as I said, I feel that PDF is getting deprecated because of insufficient demand. If this is true, then it does not make much sense to invest effort into TeX + PDF. Maybe I am wrong. Sometimes I think that I am simply allergic to TeX :)