A few of the things that surprised me so far I should mention are:
1) The menu disabling during the moogle fight. Great idea, and it's not really a problem since you can gather a lot of potions (around 20) up to that part of the game and use them during the fights.
2) The fact that Edgar comes with no tool. I couldn't predict this but at least I had bought the BioBlaster, but anyway you can buy the tools after in South Figaro.
3) The kid (or whoever it is) that block the secret passage in South Figaro before Locke scenario. Nice work around.
4) My instant death in Narshe's beginner school during Terra scenario.

5) The Gilgamesh event in the phantom train. I like the sprite and the event overall.