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The thing is that technically it isn't a proper noun - it is when Ash is referring to his own Pikachu, but not when you refer to Pikachu in general. However, since the official sources capitalize Pok?mon names even when referring to the species in general, that is the correct way to spell it.
I always capitalize Pokemon names in singular form. That just makes it easier to tell when someone is talking about one... I believe that singular names should be capitalized while plural names shouldn't, since there is no 's' following any plural Pokemon names.
I think that the singular version of it should be capitalized and the plural, lowercased. The reason for this is because there's no 's' at the end of the plural version of their names; they're spelled exactly the same.