The implementation and instruction at Khan really doesn't go against traditional teaching methods. They are traditional teaching methods, transposed online. Learn via a one-size-fits-all lecture, practice via rote. It's a traditional method, mind you, because it's worked fro hundreds of years.
I'm not surprised it works for a number of students, and I'm glad it works. It's better than most alternatives out there, paid or free, which is damning with faint praise.
I'll be the first to admit: I can't match it, or beat it, because it's a herculean effort to do so. One of my best one-day lessons has probably taken me 15 hours of work outside the classroom to write, over the course of 5 years, and has seen a half-dozen revisions. I'm still not in love with it. If I complain, it's not because I want KA to go away, it's because I want it to improve.
During my tenure there, we won the Broad Prize for Urban Education, and were specifically noted in the award for raising our 4th and 8th grade mathematics scores more dramatically than any other city in the country.