It's possible that GameFreak already have new Pokemon lined up when Generations comes out. Also remember that the anime started a few years after the first release of the video games, so that also gave them some time to think of new designs.
Also it might be possible, that it was just intended to be a golden bird in the anime, just there to show that not all Pokemon have been discovered. When they were making the Gen II Pokemon, they decided to include the bird Ash saw as Ho-oh, so Ho-oh could have been based of the anime, rather than the other way around as well.
I don't know the actual answer, but those are my best guesses.