I'm still salty over how they changed Sypha's background and made the Church--which is at war with Dracula, employs (even raised) Sypha, and also seeks out Trevor--into the bad guys for Season 1. What?! Some of this remixing of mythology reminds me too much of Lords of Shadow--it's shock theater with piecemeal nods. I just haven't been able to fully get on board with this adaptation yet.
I came to understand more or less the thought process over this (from reading Ellis works, from knowing fiction in general, from having contact with the fanbase and knowing what the bigger sections of it thinkgs).
Basically my
guess is that "good Church" is too esoteric and adding it right away risks losing the audience. Gotta appeal to the masses and, let us not kid ourselves, Castlevania's original depiction of the church is in direct conflict with what people expect from popular media. The majority of the fanbase assumed that the church was behind the witch hunts in the CV universe anyway, so the animation is just appealing to that narrative.
And don't misunderstand me, I still think Ellis didn't have the first clue what CV is about and researched the barest minimum of main points to build his narrative. Maybe he has now, but now way in hell he had when the first season was written, and he himself admited to that. But I came to understand that, if you don't want the thing with a church in it to feel preachy or to tank hard, you gotta suck on that "church authority is bad baaaad, paganism is awesome" teat, and Ellis' thing is doing exactly that. Just read anything by him and you'll see that he likes this kind of political commentary. Setting up the institution as antagonistic first would be "acknowledging" that it was no sweet flower before actually making it into the sweet flower.
But I have a hunch they will now try changing this perspective for the upcoming seasons. Maybe have the protagonists (Trevor and Sypha) change the institution from the inside, which would be cool to see. I'm very interested on those generals as the concept of them being multicultural appealed HARD to me.