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By the time the Johto journey had begun, Team Rocket had grown a bit stale and blasting them off every episode was just status quo.
I guess the writers tried to shake things up a bit by giving them a literal punching bag in Pokémon form since that's what they were themselves.
There's also the Japanese play on Wobbufett's name which pretty much makes it sound like he's just always agreeing with whatever Jessie, James and Meowth are talking about. I guess it makes more sense to the Japanese audience and their unique....brand of humor.
