tbh i think that was just you? the reason it has a different tone to the prologue is the setting. paper lily has a variety of settings, but project kat is set in a dimly lit and empty school, and an even more empty other dimension.
I don't really think its the environments. there are plenty of good environments in this game they just never let it rock long enough for it to mean anything before shuffling you onto the next thing. Like the whole illusion house segment is great but then just tossing you into a weird bullet hell sort of gimmick to climax the whole thing brought it down too much IMO. There were so many instances where I was thinking "That can't be right" because everything was over right after it just started picking up.