First and foremost: Freya is fucking awesome, and a good (rare) genuine example of a more "mature" character in the FF series. She tries to become the voice of reason, and yet has a slightly more complicated set of issues that she keeps mostly to herself. Nothing convoluted nor preachy. She's also the dragoon of the group, so props are automatically due.
With that out of the way...Final Fantasy 9.
Uh, yeah. Not my favorite, but it's not nearly as bad as some...others I can mention (FF8, FF10, FF12...or the very worst in Dirge of Cerberus).
Just about every other character drove me nuts, and I cannot to this day quite place why.
The overall plot felt...devoid of anything meaningful for me. I had a similar problem with FF5, in which nothing I did felt as though it had consequence; the bad guy(s) was always one step ahead of me because the script said so (and there was no foreshadowing leading up to some major twist or a mystery to unravel as you went along, which was the saving grace of 7) so that when I did reach the end of the game and fought the Big Bad, I didn't really find it all that believable (nevermind the colossal WTF-bullshit moment as the Final Boss Battle, but I won't spoil that here).
When FF9's "twist" did arrive, it did so far too suddenly and too late in the game for me to care; by this point, so much of the story had already focused on Garnet and Vivi with Zidane acting as a sort of "life-lessons coach" for the both of them.
On the Gameplay-side, it's one the BEST in the series (I have it just below FF6 and FFT; it's close). It's not nearly as busted as 8, bland as 10/12, nor as face-rollingly-easy as 7 (which has maybe TWO POINTS in the entire game where it's remotely challenging).
The game allows for grind-to-power OR clever approaches; which is something you just don't see in JRPGs anymore.
The characters have their own skills and roles, yet EVERY ONE OF THEM is useful at several points during the game (including late/end game; whereas in the other FF games in the series, the characters are either too similar to even classify, or a few are just so innately broken in the end game that they take over).
My only complaint here is that Freya is noticeably absent from your party for a good third of the entire plot...but that's just me.
The closest case of "outmoding" of a character is Eiko taking over for Garnet; (Esuna and Holy are just that damn good) which doesn't occur until fairly late into the game.