Or in the case of Team Rocket, are actively using Pokemon to reign terror and make dirty money.
Actually, in Ruby/Sapphire/Diamond, it was a big plot point that Teams Aqua and Magma were hunting down the games' respective Legendary Pokemon. If they're awakened and controlled, they can use them to transform the world into one more to their liking.
But given that they have the crap beaten out of them by a 10-year-old... I highly doubt their actual effectiveness
as a criminal empire.
Seriously, you'd think that once they saw that said 10-year-old is a threat (due to the highly trained death-machines under their control.), they would, you know, use guns. To shoot the kid.
You think someone who would willingly drown coastal cities is someone who would draw the line at shooting the kid in their knee-caps? Or just something so you could get their pokeballs off 'em. After which, they are a ten-year-old kid
. And you are an adult.
I mean, this is the same
problem that I had with Avatar; why get in fights with the Avatar or his friends (who are extremely
talented Benders), when you can bribe someone to stick paralytics into their tea, thus nullifying the "elemental powers" problem?
Well, other than the fact that people like watching kung-fu fighting.
Which brings me back to the fact that all villainous lairs should have some
way to knock out anyone who happens to be in any given room. I prefer giving everyone gas masks, making sure the rooms are airtight, and pumping air out of the room.