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The intelligence of Pokemon has always been a really inconsistent thing. Treating them like animals is the easiest option but many animals are simply not intelligent enough to form genuine emotional bonds on the level that many Pokemon are shown to be able to form, and it's still up to debate on whether or not house pets like dogs or cats can do so.
Generally I view them as very high intelligence animals with the mental capacity of small children, similar levels of intellect that dolphins, elephants, or parrots have in the real world.
