Thinking on it, I agree. Physical Special Split was probably the most major thing introduced. Abilities in general made a much subtler change, and natures are even subtler. However, the most "in your face" was the split.
Actually, in terms of the story game, I'd say that the infinite bag is most useful. I played the original Gen I games and I was shocked, so whenever the Infinite Bag came along was a great, yet I think uncelebrated, moment in Pokemon's History.