Final Fantasy Tactics had loads of things about church being corrupt and looking only after its own interests, members of the church believing into a (Major FFT spoilers)false prophet who they believe is the Son of God but who's actually a demon from hell, so there sure are a lot of issues in FFT that could be considered controversial. I remember hearing something like it was banned in USA for a while because of the religional contents. Final Fantasies X and X-2 also have this theme of a religion being corrupt and the leaders of the religious groups or organizations using their authority on normal people.