Ok, I'll assume you are Ben or Tom for the purpose of this discussion.
If I were in the position to really move the Khan system forward, I would focus on a few key areas. First, the teacher tools at Khan are fantastic for showing the flow of students through the material and tying in to standards based grading. But, and this is a big but, the tools for independent students are almost non-existent.
Our system is also self paced and one of the largest problems we had to solve was how to keep a self-paced system from being "I'll get to it one of these days". The Khan system, when it is outside of classroom pacing, definitely suffers from that problem. Our approach is to have the student set section or exercise deadlines for themselves, then evaluate them based on how accurately they meet those goals. It allows for flexibility in pacing but still taps into the motivation of a looming deadline. You can do this at the micro level (I will complete this exercise in 7 minutes), badge level, or group larger sections together for larger targets. Risk of just setting far future deadlines is mitigated by including data from other students to introduce competition. In addition to helping to motivate the student from a pacing perspective, it helps teach accurate estimation and integrity.
Second, and the only reason I am sharing this is because when we launch in a few days everyone will see it, is the concept of contextual notes. In our system, taking a note is not just creating a list. We tie that note to exactly what the instructor is saying and what was on the "board" when they were saying it, making the note system a way of building a reference library for each student. While you don't have to take the exact same approach we did, (as long as youtube is the delivery mechanism you wouldn't be able to anyway) you do have valuable data that you are not using to its full advantage - time coded transcripts.
Finally, if this is indeed Ben or Tom, please either fix the knowledge map or ditch it entirely. It's not helping your image to have half working features floating around.
Anyway, back to work.
-B