I think all this criticism just further reiterates how amazing Khan Academy is. Truth is that their will never be an educational system that everyone thinks is perfect. We are all too unique and absorb information in different ways. The fact that people are talking about Khan Academy at this global scale is amazing and only further amplifies it's importance, last time I checked open source education doesn't generate too much press. So instead of seeking perfection, which is unattainable, we should focus more on actually doing the littles things to make knowledge more widespread.
To that end Khan Academy has no comparable peers. Critics can talk all they want about learning theory and this and that, but fact is that Khan Academy is really helpful to a lot of people.
If you think you see a flaw in Sal's approach and can do better, than just do it and we'll see if people like it. You're into education theory, great. Keep reading and writing about education. Sal Khan is into doing, into helping people learn so that they can improve their own lives. Kindly get out of his way.
I simply ask you to watch the video, and respond to it. I think it makes valid points, and it agrees with the research I've read on how students learn (Available for free here: http://www.nap.edu/catalog.php?record_id=10126).
If you truly want to build, and learn (which I certainly want to), don't flippantly dismiss critiques. Just because all forms of effective teaching don't go viral on YouTube doesn't mean that they're invalid.