When working on PDFKit for MacOS, one short-coming our implementation had was the lack of support for Javascript in PDF's.
Oops.
(I mean, I'm one engineer and I was not going to try and hoist a JS runtime in my little PDFKit framework. And besides, the sample PDF's we were running into with JS were rare—usually tax-like forms that would add numbers from A and B and display the result in C. It seemed like a huge effort for such a small gain . Oh, and a security vulnerability.)
Arguably the biggest vuln of the filetype.