One such thing may be Vanitas' appearance. While we pretty much all got the gist of why he looked like Sora, it still was not immediately apparent and had no effect on the story at all, really. So perhaps they could extend the scene Vanitas revealing his face.
I've actually talked about this before.
For example:
-Vanitas' mask melts, revealing the uncanny features of Sora-
Ven: -gasps- Why do you seem... familiar?
Vanitas: -grins- It's that boy.
Ven: Who?
Vanitas: The boy whose heart connected to yours.
Ven: I don't understand.
Vanitas: On the night when Master left you on that prison of an island, that boy's heart filled in the gap that was left behind by me. When he took my place in your heart, we became connected through you, Ven, and I took on his form, no longer a featureless shadow.
Something like that.