I have noticed one other very slight and reasonless difference (spoiler).
I watched this video of the story mode fight with Wallace (for the King's last favor).
You'll notice that this is the PS2 version. In this video, you can hear Wallace's theme playing as he taunts the player before the actual fight. However, when I play through this part of the game on my Wii, his theme does not play until after I defeat him, when he's complaining about losing.