I really, really wish you wouldn't get rid of the missions! Having a nice circle with my progress and little boxes telling me which things I have done is very helpful for me.
I don't really like the new method, but I was happy because you could still view the mission part. Missions has never given me any serious trouble, and I just like it.
I will most likely still use Khan Academy, as it is useful, but I will be very sad. :(