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Any change Game Freak makes to the game's code, no matter how tiny, will require through debugging to make sure it didn't create even more problems. And they probably do not have the debugging software they used for RGBY. For instance, adding Mew to the game was a very risky move since it was put in the space the debugging software had taken up before it was removed.
The Old Man glitch might get fixed - that's just replacing a few water tiles. Maybe Psychic's immunity to Ghost will be too. Everything else, Glitch City, the Mew glitch. the blank move glitch, that all will probably stay.
