This is a legitimate concern and I fear whenever I hear of people lauding things like the Khan Academy without ever having used the KA themselves significantly yet. Bandwagon praise is not good and I think constructive criticism is needed lest we fall into the irrational exuberance trap again.

I think Sal and the rest of the crew at KA have been keeping this at bay by acknowledging all the good will and keeping on with the daily load of videos, enhancements to the site, open source initiatives with the exercise dashboard, and maximizing exposure with the press while not loosing vision of what they're doing or the quality of the material. That's a good thing.

But I do agree, the material on KA is a little too soft and I would appreciate more higher level material but at the same accessibility and ease-of-use as KA. OCW efforts seem to be filling this gap for awhile, but I think there still needs to be something better. Thankfully, there's Youtubers like commutant[1] who does the same video style lectures as Sal on partial differential equations, numericalmethodsguy[2] who does lectures on numerical analysis, real analysis by Francis Su[3] on the Harvey Mudd channel, UNSW lectures[4] on engineering math, algebraic topology, and digital signal processing, JimBobJenkins[5] who does a fantastic and intriguing lecture series on Game Theory, TheIntegralCalc's[6] great videos on early calculus, as well as MathDoctorBob's[7] clips on a wide-ranging list of higher maths. Abstract algebra[8] by Benedict Gross is also another class I am currently going through, really fascinating.

[1] http://www.youtube.com/user/commutant

[2] http://www.youtube.com/user/numericalmethodsguy

[3] http://www.youtube.com/user/HarveyMuddCollegeEDU

[4] http://www.youtube.com/user/UNSWelearning

[5] http://www.youtube.com/user/JimBobJenkins

[6] http://www.youtube.com/user/TheIntegralCALC

[7] http://www.youtube.com/user/MathDoctorBob

[8] http://www.extension.harvard.edu/openlearning/math222/