Two professors just released a parody video critiquing Khan Academy. Its pretty boring and too nitpicky, so you can instead read the article about it in the Chronicle of Higher Education. Their basic critique is that Khan Academy focuses too much on procedural thinking and not enough on actual thinking. This is an issue, but traditional education suffers from a similar flaw. Often, schools just teach for whatever test it is that students must take, and ignore actual understanding of the material. To properly explore a topic, one would have to hire an very good teacher to teach a small group of students who are all at a similar level. This would be very expensive. A more realistic plan would be for students to use quality interactive software to learn the material and be able to discuss it with their peers, and when needed, be able to consult with an expert or advanced student. This balanced option could probably produce the best result for many students at the lowest cost.
The other complaint in the parody is the quality of Khan's videos. It's true that Khan's videos are pretty simple, but he himself recognizes this. He stresses the main power of the site is the amount of data they have and their ability to add new features. For example, they added an intelligent quiz tool, and they will be adding additional interactivity in the future. This will improve the site, but there is also room for other players to contribute to online education. For example, if a site would make it easy for many people to create interactive educational content...
The Future of Education