Firefox is already shipping with pdf.js[1], which for me has obviated the need to have a PDF reader installed at all. And they're working on Shumway[2] for the ability to emulate Flash in Javascript.

[1] https://github.com/mozilla/pdf.js

[2] https://github.com/mozilla/shumway

The bar for forcibly disabling software on an end user's computer is very high -- as it should be.

and javascript ...