Storyline-wise, I feel there's much more to be known. the story in of itself was good, but, it felt ruched to me at the end. I agree with the Shadow Triad thing though...they need to be expanded upon I believe.
Gepgraphically, there are either areas that, to me, feel empty (route north of Castelia, think it's 4), provide very little backstory (Challenger's Cave), or both (Undella Ruins).
Oh, and other than Gym Leader rematches, Game Freak cramed in a lot of replayablility.I had as much things to do and overall fun with these games than previous ones (except HGSS).