No, there are any number of reasons why it hasn't been done yet. Mainly, most of the managers are old school. While there has been a shift in the sourcing of GMs, away from being former players and field managers, this is not true of managers. Almost all, if not all, managers are former players.
Most GMs are going to let their managers manage the game, including determining the lineup. GMs will supply the managers with data and offer certain suggestions, but they aren't going to dictate to their managers how to manage a game.
Also, can you imagine both the fans' and the players' reactions to batting Papi in the leadoff spot?
You can tell just by the posts on this board that a decision like that would receive all kinds of criticism from the fans, from the media, and probably from the players themselves. Even if a manager agreed with the thinking, I don't think he'd think it would be worth the backlash.