As much as I love my stats, I am a big believer in the intangibles that you mention. (Though some people don't want to believe that, for some reason.) That doesn't mean that I'm going to ignore what the stats tell me, but I agree that leadership, mental toughness, etc. make a difference.
One of my biggest intangible favorites is still Varitek. I don't care what anyone says about his stats (although the studies support him), I'd take him behind the plate any day of the week.