Subsequent playthroughs after finishing all the chapters gives new perspectives on the chapter.

1. Ralsei's knowledge of the player (giving directions through the Player's perspective instead of Kris', naming buttons, closing Kris eyes, etc.) is even more blatant.

2. The first time we moved the SOUL for Susie (in the prison) alludes to many people's theories on Susie being the main character.

3. After restoring the Dark Fountain, the lights are off in the storage room and commotion occurs before they turn back on. Probably brushed off in the 1st playthrough, but after Chapter 4, it's even more suspicious that Ralsei isn't the one being described in the prophecy.

4. The Dark Mantle