Since mitochondrial DNA is inherited from the mother, the best explanation for the current situation would not deal with intelligence, but rather with the reproductive success of Eve, her daughters, granddaughters, great-granddaughters, etc.
This can be explained by their being more alluring and available than their female contemporaries, thus able to attract men able to father a large number of daughters by them and to provide the necessary alimony and child support.
The Bodacious African Slut Theory hypothesizes that we are all descended from a long line of the most horny and good-looking women.
Is it?
Fathers can be influential too
Linkage disequilibrium and recombination in hominid mitochondrial DNA
Still apparently much debated, many articles online.