You do use the D-pad to set double play depth, bunt, corners in, and all the other shifts, including the OF.
I have no idea why you would need a d-pad to set a hit and run. Set your guy to steal, then swing at the pitch.
There has never been a game that makes playing the game as easy. Baserunning is so well done. All it takes is a few minutes to look at what they are trying to do.