I rate storyline's based on the "OMFG factor," which is all the awesome surprise elements throughout the story. I don't want to seem ignorant since I've only played I-II, VII-XII. Sorry III-VI. I'm also leaving out any plot details since not everyone has played the games.

VII - Although it is considered by many to be a very overrated game, it is overrated for a reason and thats because it was THAT good. Most people judge VII, from hindsight (Post PS1 perspective). I am one of those people of course and judged it accordingly. However, for the people that played it around the 98'-00' area, it was a game "above it's time." The story (although clouded at times) was epic and several OMFG factors made it a classic.

VIII- In my personal opinion, is my favorite just because it brought me into the Final Fantasy franchise. The story was clearer than it's predecessor, but also had a few clouded moments where you had to judge the situation for yourself. The romance, although nice for some, was not necessary or developed well. The OMFG factors were there, you just had to look.

X - X has always had the clearest, easiest to follow storyline out of all the games for me. The OMFG factors in this story were some of the best of them all. (X-2 just kinda ruined it for me.)

Tie between IX and X for me.
Both had a great number of twists and turns but were still clear enough to enjoy them. Too many stories are ruined by the weight of their own subtext and less enjoyable because of it.

Though I feel a lot of X's meaning was lost in the end and the wrong people were villified. In X, there were almost no real villains in the traditional sense of the word. oh, there were antagonists, but they weren't the "argh! Kill everything just because I'm evil!" kinda villain.

Actually, same is true for IX.

Final... Fantasy... TACTICS!!!! This masterpiece didn't so much have a great storyline as a great universe! Talk about depth, you could teach history courses on this world with all the information given to you. The romance of playing the righteous noble casting aside societal expectations to do what he knows is right was masterful! The flexibility of the interpretation on certain characters' true feelings, the constant swinging of the pendelum of loving Delita and wanting him to die a slow, agonizing death. These are the ingredients that make Tactics the indesputable winner of the Best Storyline award! TACTICS FOREVER!!!

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IX comes in second. Zidane's journey of self discovery was highly intriguing and provided a solid foundation for a top class plot.

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Tactics is still better...

im gonna have to say FF 9 its such a great story it just pulls me in.

It's late. I don't have the energy to bash FFXII's story.

Final Fantasy Tactics had the best plot, in my opinion. I was engrossed with everything that occured in that game. Awesome characters, tons of conflict among them, romance, etc...

I'd have to say that my all tie favorit ff story was VI. The character development was amazing, especially since it utilized so many characters. It is really difficult to develop the characters of a story when there are so many, but this game accomplished it.