Traits aren't incompatible with classes at all. In fact, Tom van Cutsem, the author of traits.js worked on the class proposal that's going into Harmony.

Aside from the simplicity argument, I didn't see anything in Markus's presentation that showed an advantage of prototypes. His point example is cloning a point and then immediately replacing all of the state, so there's nothing there that classes couldn't do (in less code).

Your gist (especially the color point) is an example of using prototypes in a way that's hard with classes. Fortunately, adding classes to JS won't hurt that at all. You could just as easily do:

    class Point {
      constructor(x, y) {
        public x = x;
        public y = y;
      }

      add(other) {
        return new Point(this.x + other.x, this.y + other.y);
      }
    }

    let p1 = new Point(0, 0);
    let p2 = p1.clone({
      color: '#green',
      toString: function() {
        return this.color + ': ' + uber(this).toString();
      },
    })

In other words, adding classes to JS won't take away anything already there. It just gets a really common pattern and makes it much less verbose. The idea is to pave the common path of class-like inheritance, but not to build a fence around it to keep you in.