This video is insane. It's an hour and a half long so it's a big one, but it's got some great history about Japan itself that I had never heard before. Really puts things into perspective.
Why Do You Always Kill Gods in JRPGs?
@icedquinn spoiler to the video, but he ends up saying that this is basically the way that the western games where you kill gods are structured, but with japanese ones it's a little different. western games are all about escalation, but japanese ones are more metaphorical and have to do with divinity being intertwined with the state. in a very condensed nutshell.