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For example, mega salamence says that has pain for the big wings, and mega aerodactyl rocks on his body hurts him

There is a good reason why megas are thanos-snapped.

There really isn't

There really isnt but but some mega forms state that they hurt the pokemon.

It was stated later that Gamefreak did that to give reason not to do Megas anymore. Either way, in a sense, the pain from Mega Evolution doesn't much matter towards pokemon wanting to do it, as it is based on the bond between the trainer and the pokemon.

yeah the pain they feel doing it is basicly just growing pains anyway

it probably feels like getting springlocked