PokéBase - Pokémon Q&A
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Title says it all.

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> The score is worked out by how fast the captures are completed and what Pokémon are transferred over. If a rarer or a legendary Pokémon is migrated, such as Mewtwo, a higher score will be given, as opposed to more common Pokémon such as Rattata, which will be given a lower score. Timing will also alter the score: if it takes longer to complete the challenge the score will be decreased; however, if it takes a shorter amount of time to complete the challenge, the score will be increased.
But, like, more specifically?
Yeah, the Bulbapedia page doesn't give a formula here :\
If you want me to turn it into a comment, I can (or I guess you could, too)

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