Perhaps Team Rocket, being the "designated and resident antagonists", are far more interesting to work with then the "goody-goody" twerps.They can do all kinds of stuff with them that you can't really do with Ash and friends. Such as slapstick humour, witty banter, surrealism or just plain getting crap past the radar. Heck, one of the members happens to be a Pokémon who can talk, which in a world where the main focus happens to mostly be on the same anthropomorphic level as regular animals is very rare, almost bordering on surreal. Not to mention that it makes interacting with Pokémon themselves far easier since they could have Meowth translate instead of having to rely on pantomime or other forms of non-verbal communication.
At the same time, it's entirely possible to humanize these characters and make up a backstory to explain something relevant to the plot. Plus the writers tend to add and subtract to their backstories, which is apparently fine with everyone because it's Team Rocket. Had this been done with the twerps, everyone would complain.
Bad guys are just easier and more fun to write for.
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