They're sequels because Iwata told them they needed to do something new if they were going to make a DS game at a time when the 3ds had already been out for over a year. Most likely they were originally going to do a grey version considering there's a grey stone item in the data like the black stone and white stone.
>"Masuda: Yes. A little later, we thought of making them sequels. When you told me that if we were going to release something for the Nintendo DS system, we had to come up with something new, I was really worried. (laughs) Then I thought, "How about sequels?"
>Iwata: For games to have sequels is nothing unusual, but we'd never taken that direction with Pokémon, so it was new.
Actually pretty bullshit since G/S were pretty much sequels, but they apparently don't consider them as such since they weren't called Red 2/Blue2 or something stupid like that.
