Indeed, several Legendary Pokemon have already been alluded to being just one of an entire species. Aside from ancient, mythical 'Mons like Arceus and Celebi, a considerable number of them could be demoted to semi-Legendary status with the likes of Rotom and Heatran.
It's disheartening to see the series become progressively more childish with every new instalment. While Team Rocket was a Marowak-killing, Slowpoke-poaching criminal powerhouse with realistic motives, Team Galactic was an incredulous sci-fi troupe which ultimately reproached its evil ways in a cheeseball conclusion suitable for a Disney flick. Similarly, as of HG/SS, the Game Corner's slot machines have been removed, and the building's sign now reads, "A safe and sound playground!" Lastly, the perverted old man who once peered through the Celadon Gym's windows and commented, "This gym is great! It's full of women!" now rather says, "It's full of strong trainers!"
Pitiful, isn't it?