The biggie is that the #3 hitter comes to the plate more often than anyone else with two out and nobody on base. Using an example, the best lineup with four Babe Ruths and five Sandy Koufaxes will have Babe hitting 1,2,4, & 5 with Sandy hitting 3, 6, 7, 8, & 9. There are some more posts scattered around about this in the Brewers lineup thread.