I think your game would improve a lot with animations. Also there's a lot of moments that could use images (or animations) to show what you are describing instead of describing it with text.
I think the sandbox gets in the way of the storytelling. But there's not much to do about it.
The story finishes and we don't know why the Fallen were behaving differently in the end. Was it not important? Maybe pointing it out is enough to give us closure.
The girls are very different but it kinda get lost in the generic interactions.
Sometimes I felt like the sub points were attached to "being a jerk" actions. This is a big no.
When fighting the kidnappers I was using guns, i was pretty sure people were getting killed. But for story purposes they were just "knocked out". This smells like inconsistency. There's no shame in winning by weapon/power superiority, no one wants to get shot.
It was a good journey. Definitively going to the "good" folder.