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Considering that in 'the past', everyone made superweapons, some of the more dangerous Pokemon actively target humans, and the fact that everyone in the PokeWorld probably has next to no policing because everyone is such a pure snowflake, Pokemon isn't exactly a utopia if someone like Ghetsis was made less schemey and much more training-hungry to actively conquer it.
Anyone can do it. You can punch out the legendaries with ease ingame, do you think you're unimpeded? Anyone can do that if they try hard enough. It's just that no one really ever realizes they can except YOU. Or in the very rare cases, people like Ghetsis.