A possible reason is to keep from lumping two lefthanded power hitters (Green and Burnitz) together. By having the right-handed LoDuca in the middle (who doesn't have power, but can get on base), you can go left-right-left, thus making things more difficult for opposing pitchers, especially when you get into the bullpen.
"One of the teams represents truth, justice, the American way, and underdogs everywhere. The other represents George Steinbrenner!" - U.S. News and World Reports columnist John Leo on the difference between the Mets and the Yankees.