There's a reason why most trainers (and "collectors") do not have legendaries in the anime. Case in point-the events in Pokémon the Movie 2000.
Exactly. But they're so cool, though!
However, I'm guessing the events in
The Power of One were triggered when Gelardan/Lawrence III tampered with specific Legendary Birds. One theory (that I dislike) is that there are more than one of each type of Legendary Pokemon (possibly barring Mewtwo, Ho-oh, and Arceus), so only the Legendary Birds near Shamouti Island could be the ones capable of escalating natural disasters if confronted. The rest might be a bit more tame...
I don't know...anyway, you still shouldn't mess with Legendaries though...insanely-powerful psychic cats, multicolored horses, and seven menacing dragons (one with a freaking
drill/TURBINE TAIL, one with a massive torch tail, and one from another world) are some of the last things I'd dare to approach without properly trained Pokemon...
If we can catch, train, and use Legendaries in the games, I guess people in the anime can, too (Championship tournaments and conferences are debatable, though)... But Ash's Pikachu will still end up pwning/tying most of them anyway, so its a moot point. :P