I think it was removed because it would be dark for Pokemon at that time period. Granted Pokemon has become darker and more mature over the years, but at the time of GSC release this would have been over the top dark for GameFreak.
I honestly think that Team Rocket has always been comic relief, and when they made them more serious it was out of place. I mean, look at the original seasons and tell me that their sole purpose in the anime wasn't for comic relief. You can't do it.
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