Giant Hole is the only case to date where the validity of the story has been questioned. While the residents of Kagome Town are afraid of the possibility that there may be a monster out there, they say that they don't really believe the story.
Black and White don't reveal anything about Kyurem. The only question is whether or not the third version will deviate from its predecessors to the extent of focusing on the ruins despite their current obscurity. Game Freak didn't do the Ruins of Alph justice in either Crystal or HGSS, but at least some questions were addressed. What the Underwater Ruins have in their favor is the fact that they probably only pertain to Isshu, whereas the Ruins of Alph are connected to various sites across the Pokémon world, if not other dimensions.