For me, nothing about FF9 really stands out as being particularly well done. It wasn't a bad game by any stretch of the imagination, but it was basically all around mediocre. Unexciting. Given adequate prompting, I could probably recite from memory alarmingly large portions of the script from FF6 or 7, having played them both at least 3 times apiece (yes, I know that's pretty bad, you don't need to tell me).
However, FF9 had some really glaring plot holes. For example, the most annoying one is that they never explain how Zidane ends up on Gaia. It would've easy enough to fit in some explanation - one of the Tantulus guys could've shed some light on the situation, or one of the terrans themselves. But no, they just basically just stipulate the fact that he somehow did end up on Gaia without any further explanation of how. While the Final Fantasy games are often criticized for being cliché and poorly characterized, one might think some subtly and assumption were in order. But, totally copping out on the story and leaving it half written doesn't really count. kelrin's suggestion that Zidane's (often annoying) altruistic behavior stems from his genetic coding to act as such is probably correct, but it's was never touched on in the plot. I doubt it really was much better in the Japanese version of the game, either. The dialogue did seem to be translated very well, for what that's worth, I think it was just genuinely Square slacking off on writing the story. It had potential, but the presentation was just kind of boring and lackluster. Given my obvious propensity for the series and for Square, to say I was disappointed by this would be quite an understatatement.
In FF7, everything was eventually explained. You could even say it was OVER-explained. FF9 is just the opposite. They basically leave some of the most important and relevant facts out of the script entirely, which sort of leaves at a loss for having a motive to play the game since, after all, the actual gameplay has not really changed since 1990.