My understanding is that PDFs are not layed out semantically, so the conversion experience is never going to get much better.
I have nothing against people who rely on PDFs for layouts, but I kind of wish in general we would stop using the format, specifically for that reason. I consider most PDFs to be a downgrade from a pure text format.
There's been a trend lately of technical authors publishing books as CSS/HTML, and I think that's a really good idea.
But I get it - if someone isn't into the whole responsive design thing, or they're not worried about readers being able to change contrast/size/fonts, it's going to be a really hard sell to convince that person to use a format that makes it more difficult to do pixel-perfect layout.