Reading over the minutes for the last W3C WG session before WHATWG was announced, the end result seems obvious. The eventual WHATWG folks were pushing for investment in web-as-an-app-platform and everyone else was focused on in retrospect very unimportant stuff.
“Hey, we need to be able to build applications.”
“Ok, but first we need compound documents.”
There was one group who thought they needed to build the web as Microsoft Word and another that wanted to create the platform on which Microsoft Word could be built.