Yeah, I think that mostly what the Flynn effect actually shows is not human evolution (as Flynn more or less is claiming) but the fact that intelligence testing is always-- and HAS always-- tested for highly inaccurate proxies of what everyone considers "intellectual/cognitive capacity."
We don't really know how to measure the real deal. IQ tests measure something, all right. But that probably isn't the same thing.
Then there's the entire concept that you can measure the capacity to do work, meaning that you're measuring the ability to deal with uncertainty.
http://www.manasclerk.com/blog/2011/03/29/the-power-of-mentoring-and-why-you-didnt-get-it/I think this has something to do with intelligence.