If they put it in the game as a means of befriending Pokemon, it's not cheating. By your logic, HP, Trainer Battles and catching wild Pokemon are also cheating.
My point is that XY, and ORAS are FAR too easy... especially with the new Exp Share (Which a lot of people do turn off)... Amie makes the easiest games on the 3DS and even the easiest games in the franchise even easier.My point is that Amie has become a game mechanic, just like Trainer Battles. It is a legitimate way of getting some extra benefits, should you be willing to invest the time, as opposed to using something like an AR to hack Sturdy or Shed Skin or Lucky Egg onto your Pokemon.
Super Training is a similar concept, but is basically rendered ridiculous by horde encounters.