PDFs for reading is one thing. Fillable PDFs are evil incarnate. Apparently there are multiple ways to do it, and only Acrobat Reader is capable of making them all work.

Then you have abominations like embedded flash...

As a standalone file representing the format of a book, PDFs are a good format. But then PDFs can unfortunately (sometimes) store much more, and then can be a security minefield.

PDFs can even contain JavaScript...

Indeed they can: https://github.com/osnr/horrifying-pdf-experiments

(Note, breakout game only works in Chrome's PDF reader)