I don't really understand what the "point" everyone is talking about.
If it's plot, then that makes every Legendary from RBY "useless;" a good number of Legendaries since then have at least a sidequest. Anime =/= Games, so no "TEAM ROCKET MADE MEWTWO!!".
If it's battle ability, then we just check the tier list.
If it's background, every Legendary has one, very few, if any, of them overlap. (i.e. Entei is volcanoes, Heatran is the Earth's core, Groudon is continents)
If it's because a certain Legendary doesn't obey the "rules" of being a Legendary (which I suspect is the main reason here), you should know there are no rules.