The brother sister idea allows for tricky things like having a split level where brother/sister have to ccoperate in order to get further in the game.
Also it allows to fool the player. Add some areas to the level which look liek a secret place. The player tries to find a way to get there with the girl, but at the end it's just a part of a level the boy has to finish later in the game. A level containing two levels so to say.