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
This is actually the root of the controversy in my opinion: the real purpose of all this online educational material (Khan academy, various youtube channels, MIT OCW, etc) is still pretty multifaceted and ill-defined.
I'm making my videos because I think that well-crafted videos make material more appealing and accessible to a lot of people on the internet. My hope is that people who are already learning the material will supplement with my videos and people who are introduced through my videos will get interested and seek out other sources. In this sense I would hope that they provide a window OUT of the "Skinner box", as would any other reasonable piece of educational material that stokes the desire to learn.
eg. http://www.khanacademy.org/video/is-short-selling-bad?playli...
The above video is supposed to be a discussion of virtues and vices of short-selling, but depending on who you are, you will tend to read it differently, because its impossible to be value neutral on that topic.
Here's another one: http://www.khanacademy.org/video/are-hedge-funds-bad?playlis...
I guess finance geeks such as myself will find the question "Are hedge funds bad" itself a nonsense question. Its like asking "Is recursion bad ?". Unless you qualify it with more metrics, such as "bad to whom/what", what is "bad", as opposed to what is "good" etc.
`Superficiality` is a strong word. Zed Shaw's LPTHW is for beginners, but not superficial. Similarly, most of Khan's lectures target a particular audience. Some of his lectures are advanced, some are intermediate, some are for beginners...just the way it should be.
Khan himself responded to one of superficiality claims here on HN(the one about history lessons).
On a related note, what many people here found a helpful introduction to Clojure was viewed with circumspection my some in the #clojure Freenode community. Assessing the quality of materials is made even more difficult by the challenge of finding the critics whose opinions are worth paying attention to.