Web Components are not yet a standard. They are primarily being pushed by Google without taking much feedback from other vendors. I spent almost a year working with building frameworks around them...and decided there was no real advantage to using document.registerElement for an Application Framework.
Again, if you want to build Web Components or use Polymer...that is fine. You can use that with Aurelia. But Aurelia's custom elements aren't built that way.
As a side note, Aurelia will be able to "export" its custom elements to Web Components. So, before we hit v1 you will be able to do that and then take an Aurelia Web Component into a non-Aurelia app and use it, the same way you would use a Polymer element. We haven't done that yet because we are focused on the application experience first and foremost.