I admire that Khan Academy is making a level-up setup. It is very lucid and helpful. However, I have a few suggestions that could enhance it.

1. It would be nice if Khan Academy makes the questions harder when you reach the proficient level. To reach the mastered level, the student should be able to master not only the foundational problems but also challenging problems associated with the same topic. I currently in Geometry, and I will be entering Algebra 2 honors next year. I want to study over the summer by using the Algebra 2 course in Khan Academy. Getting honors-level questions (after I have mastered the foundations) in assessments would help me get a feel for the subject and the rigor,\ so I can do well the following year. 
2. It would be nice if there could be partial credit involved with problems. For example, if a question has 2 parts and an individual gets one part wrong, he/she would receive half a point. Also, if the individual comes close to the actual answer, but didn't get the question right because of a silly mistake (like an arithmetic error), I believe that he/she should be given partial credit as it is fair (what matters is if you know the content, not how well you arithmetic). This should only hold true when doing more advanced topics like middle and high school math. Such partial credit can be achieved via a system that contains values that would be wrong answers to a question that are derived from silly mistakes. If a student gets an answer wrong because of a silly mistake and enters his/her wrong answer into the system, the system would recognize that the answer is wrong because of a silly mistake. This would make practices, quizzes, and tests fairer and less irritating to users. 
3. Last but not least, a final exam for each subject (like Algebra 1/Geometry/4th grade math) would be nice, along with cumulative assessments every few topics. 

Thanks for reading my post, and I look forward to learning more in Khan Academy!