Does yours detect which part of the full-text is an author name, which is journal and which is publication date (mind the reference section present in practically every paper)? Does it index the notes you made on them?

To badly paraphrase Star Wars, "your confidence in your friends is your greatest weakness". Pdf sucks, it's little more than a glorified 2d graphics api that happens to be used mostly for content that should be represented as text. Except that there are dozens of ways to make stuff look like text, but without the advantages.

This is true for some PDFs but not for academic ones produced by PDFLaTeX.

If you're really suggesting what I'm reading into your post, which is that 'academic pdfs' are somehow some sort of glorious special species because everybody in academia uses latex and all publications are typeset using that, then I have a bridge in Brooklyn you might be interested in.

PDFs don't necessarily support that. Some PDFs draw a lowercase i by drawing two filled shapes, more draw it by calling a function that draws two filled shapes. And, yes, some draw it by invoking 'i' in a font.