@Kitsune:
I haven't played Uncharted 3 so I don't know what you mean, but what I mean is that the story needs to work around the game, and not the other way around. It by no means is a parasitic relationship. Look at Xenoblade, for instance. Everything in that game's story is part of gameplay. I mean, FF13 had Lightning's gravity controlling device but it never plays a role within the gameplay, which is a small example of how story elements are NOT serving the gameplay. FF12 does decently with this when it actually lets you equip the MacGuffin weapons (but they're awful), while FF9's story serves its gameplay very well with the way Trance is worked into the story.
It's not just about attacks and powers though either. The story has to fit the context of the game. Take Final Fantasy XIII once more. Final Fantasy XIII's story is ultimately about free will and fighting fate, yet players are literally shuttled along a straight line the entire game with NO freedom to do what they want save for some imagined freedom back in Chapter 11. It's a contradiction of the story and moral it's trying to tell… in an interactive video game. :\
Very insightful post and I agree with a lot of your points. The only thing I would disagree with is your post concerning FFXIII's linear gameplay. The linearity of FFXIII wasn't so much as the gameplay being a disservice to the plot, rather the gameplay and the plot working hand-in-hand. The story or the theme of Final Fantasy wasn't a statement about fighting against fate, rather it was a question of whether or not you could fight fate.
We see in FFXIII a constant jockeying, a back and forth between people who fight their destiny and people who are victims there of. We see Lightning fighting the fate of a l'Cie yet we see Serah's fate determined by her nature as a l'Cie. Dajh contra Zazh, Cid Raines contra Fang, they game is filled with characters who suffer their fate as well as those characters who strive to fight against it. Even the ending has no real "everyone wins" set-up because with regards to Fang and Vanille, one might say that in becoming Ragnarok and destroying Orphan's Crib, they completed their focus, hence the reason they turned to crystal and still remain in that state. Right up until the end some characters have free will while some are still puppets of their Focus.
Just because a character tries to exert freewill that doesn't mean they will succeed, and just because a character believes they can fight against fate, that by no means assures victory. Now of course the real reason for the linearity of FFXIII's gameplay was piss poor design, which I won't deny, but if we're going to address this from the perspective of story line, XIII wasn't about the expression of free will so much as it was the struggle to attain it. In the same way the characters had no control over where they were going in their adventure, the gammer had no control in that regard as well.