Lots of reasons. If encryption is ever to become widespread, it needs to accomodate the myriad of situations that users might need computing/communication in. Which is a lot.
I've seen this implemented (in a very special case) with statically-linked GPG on a USB drive and a Crypto Stick[1]. Better than JavaScript (because you don't need to rely on an untrustworthy interpreter), and the keys never leave the smart card. The big limitation is that you need admin access to the system if you need to install drivers for the smart card.
[1] http://www.crypto-stick.com/