My quarrel isn't merely with the portrayal of men or women, but the portrayal of their relationships and interaction. It is found throughout Moffat's work, in Coupling and even Jekyll. There is a definite "battle of the sexes" edge to it that was not in the classic series.
The Atlantic took a look at Moffat's gender politics in Who a few months ago, and they chart it going back to "The Girl in the Fireplace." I think part of the problem is that Moffat's characters are more plot puzzles than characters.