...that was one reason, but it was hardly the only reason. The circumstances are much different here, you realize, not least of all in how Team Rocket relates to Johto as a whole; regardless of how much you happened to dislike either set, I'm sure you can appreciate the difference between a group of individuals with the military in their pocket and an organization dedicated primarily to petty thievery.
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You know, you're not very good at being subtle.