but didn't these hints come up waaaaaay late in the arcs? The manga isn't like the anime, in which it'll show a preview Pokemon like two years in advanced. The silhouetted Lugia and Blue bringing up her Bulu only occured at the very end of the Yellow arc, not long before Gold/Silver's release. Likewise, the Houen region was never mentioned until Crys made the assumption that she completed the Pokedex at the very end of The Final Battle.
Although... considering Yellow had the Rainbow and Silver Feathers on her hat all along, the main characters just happen to have several Pokemon that would be given new evolutions in the next generation (Green's Strike and Porygon, Silver's Nyula), and the whole issue with Silver trying to find his parents, I am left to wonder how far in advance they plan these storylines, considering these small points stretch out all the way into the next generation's story arc.