The 3-hour Roxas prologue
Aerith's voice
Simba's voice
Nala's voice
The absence of "What's This" and Christmas-themed costumes in Christmas Town
The last Port Royal boss
The time limit in the fight against Demyx
Simba: Cam Clarke also voiced Simba in Timon & Pumbaa and The Lion King 1/2, but he did a much better job in those.
Nala: Vanessa Marshall never voiced Nala before. I don't know what they were thinking when they cast her.
Aerith: Absolutely no emotion in Mena Suvari's delivery. It's like she wasn't even trying. Correct me if I'm wrong, but doesn't she do a better job in Advent Children?
I'm looking for a high quality AVI or WMV of the scene where Axel says "Got it memorised?" I looked through this site's whole archive, but it wasn't there.
Edit: On second thought, I think the scene where Cloud yells "Shut up!" would be better.
