It isn't actually better games. It's lazy reuse of tropes, character archetypes, and mechanics. Killing God was okay when Breath of Fire 2 did it because it was kind of newish in the West at the time. However, when you get to the 30th RPG where the Western-styled church is evil, it fails to be interesting.
I agree with the core of your point that everyone is just lazily recycling from each other, I would say animation has shown this even more blatantly with how many people were "inspired" by anime in the west but don't actually get how to make the anime that they actually liked or why it was good in the first place. They always miss something, and just lazily copy paste the cliffnotes with some small twist if that.
But I'm of the opinion that at this point in history writing is just always full of tropes and archetypes if you look hard enough. You can just always see things that tie into older works and became a trope over time. These things are all varying degrees of (usually) exaggerated looks at the real world or concepts in the real world you could find. "Church bad" plots are effectively observations of corrupt churches who either have mislead people on its teachings using higher illiteracy levels, or about seemingly holy people being unholy because they all into a vice. This is obviously ignoring people just writing about their hatred of religion as a whole, but those types of stories tend to be far more issues than just writing a lazily written bad church like the types of games I think you're talking about.
Almost everything that could be said just has been said if you dig deep enough somewhere, we're all just trying to make them interesting and obviously many fail at that. In a way true originality is dead if you want something that would be consider normally coherent.
You can have "church bad" be worthwhile if you actually do something with it, the idea isn't inherently bad, it is just lazily written because it doesn't take too much to put a church in power and then abuse said power. You can replace church pope man with politician/world leader or a dictator and it'd be pretty much the same thing really with some word changes.
Fighting God is just an exaggerated version of fighting "the root cause of X problem", or as some zoomer might call it "the CEO of racism", for a more epic and dramatic effect. It is a simple climatic way to end a story where if you defeat X you will begin a healing process for the world, you don't need God for it and it'd be pretty much the same idea.
So I guess my (probably unpopular) take is that, no concept no matter how cliche it seems today is inherently bad, it all just depends on how you write it and what you want to use it for. You can still make killing God at least decent even if 90% of attempts in the past 20 years are boring with it. The problem I find is many people are genuinely inspired by better works of the past, yet they are just lazy enough that they don't get why the stories they like actually worked. It is like trying to write your own Hamlet without knowing why Hamlet was even good. Hamlet to this day is still a pretty good story I'd say, but if someone just ripped off Hamlet badly and failed to comprehend what made it good, then they're just an uninspired poser who took Hamlet's character archetypes and tropes and made a bad Hamlet.
I think (in animation) RWBY is the best example to explain of someone who doesn't get why the works they're inspired by were good while their copy work is so poorly received.
