I disagree with your disagreement about the religious symbolism not being handled well. Two scenes I've ever heard you harp on and neither scene is actually important, hell the crucification scene is hardly one of the big moments in Disc 2 and largely serves as explaining Elly being taken. It lacks the symbolic significance like Xenogears' birth, the one winged angel statues, and Fei's journey largely being a parallel to some Gnostic takes of Jesus. Many of the religious names utilized are not haphazardly given out to sound cool (unlike a certain seventh installment I can talk plenty of smack about for abusing good writing for the sake of shock value) but instead bear significance to the characters role in the story. Honestly, you won't really find a series outside of maybe MegaTen that handles religion with such historical accuracy for its themes, mythology, and values.