The problem is that people build this huge, powerful libraries, but nobody seems to write the "limiting" libraries that take a subset of the powerful base library and create an easy to use experience from the user.
I suppose this largely stems from "implicit knowledge": People who can write cryptography apps likely know enough crypto that they can't themselves identify usability problems.
Huge does not mean powerful when it is hard to mix and match (and limit) the functionality.
1) libraries are often too complex for the avg dev: well, crypto is complex and there is rarely a one-size-fits-all solution. however, there are high level APIs that address your issues in openpgp.js (https://github.com/openpgpjs/openpgpjs). problem is that a lot of people try to roll their own crypto if the library does not offer those high level #box() and #unbox() functions. and THAT is a real problem down the road.
2) lack of empathy is really a big problem, which I've articulated here: https://blog.whiteout.io/2015/01/29/why-alice-has-a-problem-...