1) the problems of having to teach users how to enable Java applets. Having done time on a customer support desk in a past life, I know full well that talking someone technologically inept through something like that would be hell on Earth.

2) and a point about how this idea works out less secure in practice as you're allowing 3rd party code to run natively on your machine, desensitising users to running 3rd party Java applets (or even encouraging people have the enabled to run by default). And scripts running inside PDFs are a known vector for attack as well.

I also disagree with the practice of pushing proprietary solutions which are only able to work on a single platform - which it sounds like their solutions are in-spite of Java and PDF being open and cross platform standards (I'm having to take the OPs word on that point - as I'm not a resident of the same country)