More is Different and Less is More
What does seem to have changed in those brain genes is that their expression has be up-regulated - in some ways a human brain is just an overclocked or increased displacement chimp brain. This is not terribly surprising if one considers recent progress in artificial neural networks - the main difference between the neural networks of twenty years ago and the modern, super smart ones is scale - the number of neurons (nodes) and interconnections.
One prominent difference between chimps and humans at the genetic level is in the genes expressed in jaw musculature. We have lost the gene for powerful jaw muscles. Why? Maybe to make room for cranial expansion to accommodate those increased displacement brains. We have lost a number of chimp genes.