One thing about the prologue nags at me story wise. At first it was a small thing, but the more I think about this game, especially after multiple playthroughs, it grew to nag at me more and more. Before I go on though, I do want to say that the story for this game is superb. It has layers upon layers contained within it and it was a joy to play. This is by no means a complaint, just something that nags at me a bit.
What I'm talking about is the fact that Jaye essentially ended her friendship with the MC as it existed because he overheard a conversation and agreed that she should find friends of her own. Now, I can see this changing some relationships if adults or even a teenagers were involved, but essentially ending them? Also, remember they were TEN at the time iirc (met at eight years old, two years later is when the conversation is overheard). I keep thinking to myself, what are the odds a ten year old will essentially end a friendship as deep as theirs was over something that lasted only a day or so? Especially since they're together every day of their lives.
I've raised two kids. I've helped raise at least a dozen others (my wife is one of eleven, heh, there were lots of nieces and nephews). A ten year old rarely holds a grudge even for a week, let alone forever. It doesn't really add up. I have to assume it was artistic license to make the story work as a whole, which is fine. But still it nags at me.