More or less applied to the anime too at some point, in a weird way.
It appeared in the first episode of the show, couple years before the second set of games came out. Probably as a way to hype the next generation up as it was never followed up on (maybe the old director talked about his plans for it but I'm not too knowledgeable in the anime to make that claim.)
I know Lugia had it's own movie eventually (and now is getting another), but with the way Ho-oh showed up in the show along with the fact that the beta GS didn't have it all. It makes me think that originally GS were gonna have just one big legendary with the legendary trio, similar to Red/Blue and it's handling of legendaries (not counting event mons like Mew.)