I haven't spent much time thinking about Khan Academy, at least compared to some people, and even less looking at it. My thinking on the topic is pretty well illuminated by a review of Jeff Dunn's Evolution of Classroom Technology post. If Khan Academy is a big deal, all the things leading up to it should have been bigger deals too. There should be a more prominent 40 year track record of programmed instruction and audio-visual aids leading to increasing achievement. There should be lots of pilots with more expensive and clunky technology (extensive libraries of VHS tapes going home with kids, etc.) making the point that if we could only find some practical way to distribute this stuff, the amazing results seen at a small scale pilot would explode across the country.
That's just not what happened. It is all somewhat effective, just not dramatically so. Evolutionary changes. Sustaining innovations!