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"Cheating" for online generally goes into generating Pokemon for use in competitive play. It would be very closed minded for Gamefreak to reject a competitive community that doesn't want to spend ten thousand years IV and EV training for a specific moveset, ability, and nature. This is especially true when many pokemon later on become more useful with a different moveset than what becomes "established" and you are left with a lv.100 IV/EV trained placeholder in your boxes. It also limits the variety of pokemon used in each metagame as people would only take the time to train a limited amount of pokemon (unless they had nothing to do but training I guess.)
Now, some people can argue that it takes away from the friendship and bonding aspects of the game, but this is a moot point as those mechanics are still there if an individual chooses to use them. It should not be an enforced policy.
