I'm sorry what? Why would you link and then judge all of 2.0 if not all the rest of the game based off on an introductory quest line that up to you becoming an emissary would be if Pokémon had a different story starting point based on what your starter Pokémon was. That made its way to facing your first gym leader. While never seeing what the other two openings delt with. The reason why the crystal is blue is a nod to the rest of the Final Fantasy series where if the game has you collecting crystals it's almost always a blue one. I'm going to assume you ignored the obvious not physically seen power up that should have happened soon after picking it up.