I've been working on a JavaScript API for Skype, https://github.com/oskarer/skype-js, utilizing the same endpoints as web.skype.com. Features currently working are login, receive and send messages. I have little time to work on it but it definitely shows potential.
This project sounds interesting!
Would you consider reverse engineering the Chrome plugin to add calling? (https://chrome.google.com/webstore/detail/skype-calling/blak...) Not sure if the plugin uses native code, but it should be possible to grab the mic / play audio from terminal.
The web gateway is somewhat unreliable, and for IM purposes 'useless' compared to the MSNP gateway, which seems to be the main one used by official clients nowadays.
It has less documentation, but still is plaintext-over-TLS, unlike the legacy (and, arguably, less reliable as well) supernode protocol the poster has been reverse engineering for the past years.