Sorry for the spam y'all, I keep falling behind on this!
#12 - We finally got to see and interact with the people of a lost civilization that was presumed dead throughout this franchise's long history.
#11 - Whether you face the embodiment of destruction or the embodiment of life, in both of them you're trying to prevent destruction.
#10 - This game was criticized for having its main quests be too repetitive and samey looking. The developers heard the complaints and ensured that in the sequel, the main quests were repetitive and different looking!