True but I think even just one would be serious trouble. It's a huge, metal beast with intelligence that surpasses humanity- it'd be extremely difficult to take down.
I honestly think though a world with Pokemon wouldn't actually be that bad. People say terrorists and such would use Pokemon for evil acts- but would they waste their time levelling a Pokemon to a powerful level or would they just use explosives/guns/whatever. Using Pokemon could be considered a difficult and long alternative to using actual weapons.
I have to agree with Nimburst, Metagross seem to prefer living in seclusion rather than mix with us crazy humans. Which seems to suggest that they are intelligent enough to know that we're nothing but trouble, lol!
And even if one did show up, it wouldn't be that tough to deal with it. Sure, they've the intelligence of supercomputers, but they're not omniscient or anything. Just have some friendly Ferrothorn set up Stealth Rock traps around whatever populated area you want to protect to alert the citizens of approaching Metagross, and maybe throw in some Leech Seed booby-traps for good measure to slow it down/weaken it. After that, a few quick Earthquakes or Fire Blasts should be enough to encourage it to go back home. Between the harassment it would get from humans and trainers and the sheer number of humans it would have to deal with, they wouldn't be much of a threat.
I should think that Rotom would be one of the worst Pokemon to fear, if it ever decided to gather in numbers and actively take over the human race. I mean, the ability to possess anything motorized is pretty scary. Similarly the Porygon family would be pretty frightening if it ever decided to wreak havoc on humanity, thanks to their ability to enter computers. Now that I think of it, that would actually make them the perfect counter to any angry Metagross wandering around!
Still scary but slightly less frightening would be weather summoners like Tyranitar, Hippowdon, Abomasnow, DW Ninetales, DW Politoed, Castform, etc. Just because they could devastate any environment they entered.
And lets not forget dear old Shedinja. All it would have to do is learn to float backwards towards people, forcing hundreds of innocent human souls to be sucked into its carapace...
I do think that Ninjask would be considered an evil Pokemon, and training or evolving a Nincada would be against the law.