As a whole, I feel the sequel is an improvement. However, when it comes to personal taste, I prefer the CGs in the original while I prefer the animations in the sequel. As far as which stages I prefer, I'm gonna say the sequel's rendition of the lost village is an incredible moment. While I still have a lot of love for the background art for the original village the sequel definitely has more of a Resident Evil 4 vibe going for it. I love how the villagers appear 'normal' at first till you're first captured and it all goes downhill from there. Defeating the cultist priest there was my fav boss battle, too, since it feels like the stakes are already high when most players on their initial playthrough will get captured by it, beginning the parasite arc.
So, with that said, it kinda feels like fighting the cultist priest feels a bit more personal, you know? Especially when you fail the first encounter and it's a race against time to defeat that evil before you become part of it.