Just a few thoughts I had on the manner:

Could the Al Bhed be seen as a kind of Jewish figure? They are constantly persecuted by the rest of Spira much like the Jewish, eventually finding a "home" is Isreal, or in the case of the Al Bhed Bikanel. Home is then destroyed by those with other religious beliefs, much like what has happened and is still happening in Isreal today. Not to the extent of complete destruction, but parallels could be drawn.

And also could Yuna be considered a Mary Magdalene of sorts? While it's never been confirmed that Mary was Jesus' spouse, there's a lot of theories going around, most sparked by the da vinci code, but maybe I'm just plucking at straws here.

Also could the Aeons be seen as Angels? They come in a sort of ethreal form and aid and guide our heroes, with one coming to Tidus to tell him of his mission. This has parallels with the Angel that came to Jesus to tell him of his saving of the human race and persecution by the Romans.