We attach moral terms like "fair" and "unfair" because we want to romanticize what we do, but, just like in real life, the most important function of the rules is to give people an absolute leaning-wall from which all future decisions can be made, rather than, in the real life example, the arbitrary state, which makes decisions as they come and can't be predicted. I don't approve of the lack of sleep clause in Free Mode, for instance, but having made it so already it is in Game Freak's best interest to leave it as it is instead of editing the game because a certain party thinks it's unfair. Although I am fascinated by tiering debates on Smogon and like hearing both sides of the argument whether or not I agree with them, I think Game Freak's adamant "We're not changing anything" stance is better in the long run.
Of course, I still agree that they never should have ditched the sleep clause in the first place, whether or not it is wise now for them to change it back the way it was.