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I hope some mega evolutions will be retconed to regular evolutions, explain that they found how to evolve them permanently.
Pokémon that has not sense to evolve except for megaevolution (lines with three Pokémon, Kangaskhan, Diancie...) would keep the megastone, while the others (Mawile, Sableye, Audino...) would evolve with modified megastone.