Luminous Arc: Like Star Ocean 3, Christianity is depicted in a negative light. The Church are the bad guys along with their "God", whatever that is.. I am near the end of the game, already defeated the angel (a mischievous girl who does nothing but cause trouble) but haven't seen how their "God" looks like. Once I finish this game, I will be playing its sequel which has a new feature: engagement with witches to gain powers when both parties are in a synchronized state of love. And once again, the bad guys would be..
Persona 2: Tsumi: The prequel to Persona 2: Eternal Punishment never made it outside Japan because of the story in which depicted the protagonist as the reincarnation of Adolf Hitler. I haven't finished the game yet but I think it has something to do with reviving the Nazi. On a second thought, up to my last saved point, this definitely doesn't seem to be the case. Then again, the idea that "the protagonist was the reincarnation of Adolf Hitler" alone shouldn't be all that controversial, unless the Jews were complaining about it, then I guess that answers the question as to why it was dropped.
Persona 3: FES: This one also depicts Christianity in a negative light. The leader of Strega, Takaya is well-known as Revolver Jesus in some circles. Apparently, the guy is depicted as the leader of some cult in which people faithfully follow him, thinking that he is some saviour to save the world and I still remember Takeba Yukari saying, "It makes me sick to hear that teachers are encouraging students to join his cult without knowing that man's objectives.." Obviously, she got a good point. Some people are blindly following religious beliefs without ever stopping to think for a moment. Then again, I am assuming that those religions unlike Buddhism that promotes people to challenge it and gain enlightenment, it is the exact opposite.
Star Ocean: The Second Story: In the US version, the names of the antagonists who were named after angels, such as Gabriel (were changed to Indalecio), Metatron (were changed to Berle), and Lucifer (were changed to Cyril) obviously because of the religion-related sensitivity. However, perhaps time has changed since a decade ago because they decided to keep the original names in the new enhanced psp remake: Star Ocean: Second Evolution.
Star Ocean 3: Till the End of Time: I have beat the game a few times and I know the story pretty well. Generally, it depicts Christianity in a negative light. I could list all the points by heart but that would take too long, so I don't plan on doing so now..