(This contains *SPOILERS*)

This is strictly my opinion of course and if you don’t agree with it that’s fine.

1) Make Stefano Valentini the main antagonist
Until Myra deals the final blow on him when he attempts to kidnap Lily again.
I think Father Theodore is not really needed. He is a generic religious fanatic with the “join me or you will suffer” line. 
Stefano can be the one who does the guilt tripping instead of Father Theodore after he found out about Sebastian’s past. He can turn Sebastian’s grief and guilt into art and possibly tormenting him by threatening to hurt Lily. (He won’t kill her of course because he would lose his powers if he did)

2) Liam, Julian, Yukiko or Esmeralda should live
Some people can predict their deaths. It would be less cliche if at least 1 or 2 of them live.
If Liam and Yukiko live they will probably join in with the plan of taking down Mobius.

3) Make the vision sequences with Lily playable (the part when Sebastian pick up Lily’s doll and it trigger visions of Lily running and hiding)
It’s scary when you play as a defenseless little girl being chase by a serial killer and monsters.

4) Kidman and the Administrator should have a final fight.
Seriously, towards the end the Admin just stood there and just talk to Kidman? He didn’t attempt to stop her himself? Okay, maybe he prefer his goons to take care of that for him and that he did attempt to control Kidman using the chip but failed. But him dying in the end via chip in his neck that malfunctioned when STEM shuts down is anticlimactic. Why does he have a chip in this neck anyway? He’s the boss. I thought the chip is for him to control his employees.
He could still make a last attempt to stop Kidman after his goons died.
But I could be wrong though, maybe the Admin as the name implies that he’s only an admin but not the actual Mobius boss.