PDF is a format designed for the exact display of documents, not for anything else. It's like ranting about your printer losing all those html tags semantic when printing a web page. The pdf format is not to blame here.

Convert to PDF can be very useful for generating reports. For instance, you display a chart using Javascript, and get exactly the same chart in the generated report.

We use EvoPDF for this purpose, which also uses a website based webbrowser under the covers. Unfortunately it is quite slow, especially when Javascript is required for the report. It also handles tables badly across multiple pages, and full page backgrounds are also cumbersome.

There's a pretty good reason for scientific papers to be published in PDF. First of all TeX was originally designed to work with PostScript which was intended for communication to printers, so the step to PDF was easy to make, second of all PDF has had fairly broad support and unambiguous representation for longer than HTML has (and even though HTML appearance is now somewhat standardised it's still nowhere near as stable as PDF has been).

PDF stable? The only party that properly renders PDFs is the one that came up with the format, it's as bad as Microsoft Word in terms of interop.

That it is a supposedly open format is a joke, there is so much old cruft in there that you could implement if you had access to Adobe's source code but unfortunately nobody but Adobe does.

PostScript (which PDF is a restricted version of in many ways) is clean, but PDF is not.