Once on the train you push a button on a light up map of the stop you want. It stays lit like on an elevator, the train only stops at the lit up stops or the ones where someone is waiting for a train.

This way trains never stop and open their doors then just sit there wasting everyone's time while no one get on or off.

To avoid trains backing up in the tunnels the platforms should be split into two or three levels so more than one train can pull into a stop.