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I feel like people just haven't seen it in a while. He was wrong because catching those pokemon was fucking up nature. I think that's a good enough reason to stop the villain.
But that in itself is a weird message because it's essentially telling kids you shouldn't catch certain Pokemon. But the show also made kids concerned that evolving Pokemon might be bad, and you specifically weren't supposed to catch Pokemon in the anime's Safari Zone, so I guess it was just contrary to the games sometimes.
