First is the model/API for actually writing your app. Web Audio is very imperative and, in my experience, doesn't handle dynamic behavior terribly well. Elementary is designed both for functional/declarative expression and for change over time.
The second piece is that Elementary is built around a core runtime which can be embedded anywhere. Web Audio is, as its name might suggest, quite coupled to the browser environment. My goal is that if you've written an audio app that runs at the command line with Elementary, you could package that same thing up and ship it as a VST plugin, on embedded linux hardware, etc.