My problem isn't with PDF itself, but that it's overused in places where it really doesn't need to be. Academic papers are the big one, where HTML would almost always be a better choice. What's even more maddening is that papers aren't written using Adobe's PDF tools, they're written in TeX and then converted.
If you're an academic reading this, I implore you to please publish your papers in HTML (alongside PDF is fine too!). It makes them far easier to read, as browsers can reformat the document according to the readers needs.
PDF is a type-setting format for ensuring print-accurate documents. Please stop publishing content that is meant to be consumed online in it.