That's because the WebGL version is using your GPU and the Flash version isn't. The Flash version is done through the 2D drawing API which is equivalent to HTML

That's because the WebGL version is using your GPU and the Flash version isn't. The Flash version is done through the 2D drawing API which is equivalent to HTML5 canvas (i.e. CPU bound). So, in that respect, the Flash version is actually doing a pretty amazing job.