Actually, I had some interesting thoughts earlier. This is kind of a silly interpretation of a few minuscule things in this game, but it's interesting anyway.
There are a few pieces of evidence that Final Fantasy has an anti-god (not particularly anti-christian, but anti-god in general) feel to it:
First, I will point out that the final bosses of FF6 and FF7 resemble stereotypical god-like figures or angels, and they are both fought in this atmosphere that resembling the stereotypical image of heaven, floating in the sky with clouds all around. The FF9 boss has a few god-like qualities to it as well and is also fought in a heaven-like atmosphere up in the sky.
And at the end of FFX, after you fight the main final boss battle, there is a small and easy battle with Yevon, who is a religious figure--a deity of sorts--to many of the people in the world that the game takes place. He doesn't resemble the imagery of a god though (I vaguely remember what he looked like, but I think it was something like a scarab, or The Tick's insignia, or something).
This one is a bit silly, but just for giggles I'll mention the FF4 boss. This boss looks just downright wierd and is fought in a very bizarre yet intense atmosphere. However, his most powerful attack is called "The Big Bang," which associates him with creating universes. Yeah, that one is kind of silly to mention, but oh well.
They seem to have some kind of fascination with defeating gods. I've never seen the FF2, FF3, FF5, and FF8 bosses, but all of them I have seen have at least a minuscule reference to gods or deities.
Lastly, which is more relevant to Christianity, there is Kimari's ultimate weapon in the game. In the American version, it is called the Spirit Lance. However, this isn't the original name of the weapon. In the Japanese version, it is called Longinus, which is the name of the Roman soldier who pierced Christ's side with his spear at the end of his crucifixion. My guess is that they changed it with the English translation so that it would sit better with an American audience, which is vastly Christian.
These aren't that big of a deal, but they are interesting speculations that I thought might be fun to point out.