I'd be more inclined to agree with you if Pokemon itself was a very story-driven game. Have you seen what Game Freak has come up with when they try and make a deep story? It doesn't turn out well. As for the Pokemon themselves, Johto was more of an extension of Kanto as opposed to an entirely new region like Hoenn or Sinnoh was. It's perfectly expected that they would be expanding upon the older 151 Pokemon in this game. And yeah, it's fairly linear. Most Pokemon games are. Elm is half a professor? Have ANY of the professors been of any substantial use yet? I think not.