Alright, I've been doing Khan Academy classes for almost three years now, I am no stranger to this website and its flaws.  For this, I won't even go into all of my numerous issues with the videos and will be focusing on the math sections here, as math is all I've taken from this website.

1. The overall course structure

Simply put, the current system just doesn't work.  I haven't learned a thing from Khan Academy in the three years I've been using it exclusively for my math education.  The only reason I actually passed geometry and am passing algebra 2 is because my parents found me a tutor (my school has its own host of issues in regards to the math programs there).  I am forced to take these 'classes' as part of my high school curriculum but they simply don't work.  They are structured terribly.  An example of online learning that is sustainable would be Dulingo because, for all its issues, it does still encourage learning.  The way that website is structured is infinitely more sustainable than this one.  For starters, it allows you to cycle back through problems you've already completed or skip ahead and do more problems and go back later if you get stuck on one particular thing.  I find that system could be incredibly helpful for this website, as I find my tutor and I will take screenshots of the 'Hints' and look through them later if we get a similar problem and hope that it will be slightly less confusing.  Honestly, just offering the option of arrow keys in the corner that let you cycle between problems would be immensely helpful.

2. Double-standard and confusion in questions and answers

Sometimes an answer needs to be simplified, sometimes it doesn't.  Sometimes the fact that an answer needs to be simplified is stated above the answer box, sometimes it isn't.  That's just flat-out sloppy design.  Next, why are some of the questions so complicated?  And does every story problem need a name that looks like a keyboard smash?  Why not just use the names 'John' and 'Jane' or something simple and call it a day?  You don't need 'Andersmithonson' in half a dozen problems to get your point across, it just comes off as distracting.  Also, I know that variables besides X and Y exist, but do you really have to change the variable every single question?  It's infuriating to get a question right and get docked for using X instead of Z in your answer on accident.

3. Energy points

Just, why?  What's the point?  What purpose do they serve?  I don't feel special for having 600K+ energy points, I just feel like I'm on the receiving end of a tacky, pointless 'reward' system.

4. No penalties

On the opposite end of the spectrum, there's no penalty system for failing to do X amount of assignments a day on Khan Academy.  This is why geometry, normally a 2-3 term course, took me 2 YEARS to complete.  I didn't feel any reason to do any work.  Now, this isn't just a Khan Academy problem.  This goes out to all online education in general.  But, when the education and futures of children are on the line, I think a little more thought should go into ways to get people to log in every day.  Perhaps if Khan Academy had a genuine grading system and not percentages this would work better.

5. Assignments

Khan Academy doesn't have traditional 'assignments', it has what my dad likes to call 'modules' (though I've also heard people refer to them as 'sections').  Basically, each 'module' has a set of problems for you to 'practice'.  You can do these 'modules' in any order that you like and at any time you would like to.  Simply put, this is a horrible system.  I feel the website could work with a complete overhaul of its content.  Compile these 'modules' into makeshift 'tests' and 'assignments'.  Assign them in chronological order because, like my dad always says, math builds upon itself.  When a person starts a Khan Academy course, give them a 'test'.  This 'test' should asses their knowledge of the material, consider it a giant 'Mastery Challenge'.  Once the 'test' is completed, compile a structure for the course that makes the most logical sense.  Person 1 already knows A and B, so now we will teach them C,D, and E in that specific order, etc.  Rather than having 'Practice' and 'Mastery Challenges' how about instead create an E-textbook.  Put the equivalent of a few 'Hints' sections at the beginning of each lesson (and allow the 'Hints' portion to be available while the user is doing assignments) , walking the user through how to solve the problems.  Then follow it with a list of problems, either all on the same page or on a few different pages with the ability to scroll back and forth through all the problems.  After the user has completed a 'Unit', generate a 'test' based on the 'Unit' and have the user take it.  If the user scores 75% or greater, they can go on to the next 'Unit'.

Overall, Khan Academy has some good in it, but it lacks a good way to distribute or even display that good.  Take a good look at these suggestions, you just might find some good ideas here.