My complaints about the Post FF6 state of the Series have never been that they went too 'emo' or something. After all, there's often perfectly good reasons for people to have their minds in a dark place sometimes. My problem was that, due to lazy story writing, the attitude never seems... Justified. For example, Final Fantasy Six has an actual SUICIDE ATTEMPT by a main character, but at that point in the story, it was perfectly justified by her father figure, and as far as she knows, the only other living person in the world, dying.
Cloud, in 7, had a reasonable reason for having such a twisted negative personality, and that was that he didn't actually have a personality, but a half-assed simulacrum of other people's personalities meshed together. He wasn't so much emo as much as he didn't comprehend how to behave naturally...
But what about Squall, in eight? What the fuck was his excuse? From the very beginning he acts kind of like a dick to basically everyone he meets, despite everyone he meets actively being nice to him, save for the villains. Never mind the other story writing problems that fill that game and bizarre out-of-character behaviors, and lightning fast passing of the idiot ball, that the story relies on to move forward. (A trained sharpshooter and sniper whose been in your party for hours killing things for you suddenly locking up an unable to fire on the Sorceress? Did no one screen this guy for the allegedly well planned assassination attempt? Or did they just hire the first guy who walked in with his own gun?)
This is also the point in the series where it begins to suffer from Alien Space Flea syndrome. While in the other games up until this point, there was usually a greater threat beyond the one you think is the threat in the beginning, some monstrous evil power manipulating a lesser villain, before you usually learned of that early on, or at least half way through the story. In 6, for example, you had the Empire you fought against in the beginning, before Kefka makes his move and seizes the title of the Big Bad. In Seven, while you're fighting ShinRa Corp., Sephiroth and Jenova are key elements of the story long before you ever actually meet or fight either of them.
In eight, Queen Ultimecia seems to come out of nowhere, though mentioned a few times before the final confrontation. Her role in the story is poorly defined until late in the game, removing the sense of foreboding one might have had in FF7 when you cross through the wake of death left behind by Sephiroth.
FF9 just felt disjointed and random without any coherency as to what was going on. While an attempt to get back in touch with the series roots, I never felt like anything mattered and the characters were just poorly characterized, with a few exceptions, but bizarre character designs and storytelling that never really went anywhere or felt anything approaching epic killed it for me.
Ten? The ongoing narration by Titus and the repeated attempts to beat you over the head with the themes of the story were annoying, but even that didn't kill it for me. What killed it for me was again, the lack of coherency of anything. Look at their design choices for instance. The bizarre dress of most people in Spira can be handwaved away, that's fine, but then you have the fact that you have characters like Lulu, who, despite allegedly being native to the world, seems like a square peg in a round hole. She doesn't look like a native, is the only person who dresses like... That. Wakka is the only person in the entire world with a Caribbean accent. No one else, even in the same village shares it. Where the hell did that accent even come from?
You have transparently evil characters like Seymour, whose success again relies only on the fact that everyone around him is carrying the idiot ball. This also had the absolute worst Alien Space Flea infection, what with the final boss being a weird floaty black thing inside Sin that was never mentioned before, or afterwards. The only real, interesting boss fight in the entire game is the one against Jecht near the end of the game. In fact, if they really wanted to make the game's themes really tie together well, they would have set it up through out the story to make THAT be the final boss fight. It would make Titus' narration about how it was 'his story', actually sound not egotistical.
11 is an MMO, and doesn't count. Same with 14.
12: I've already gone to some lengths to describe my problems with 12 in another, older post. Primarily, it is the inappropriate insistence on having Vaan as the main character when he both isn't the main character of the story, and doesn't make sense as a party leader, particular when the other possibilities are, Charismatic Pirate, Grizzled Military Captain, and Royalty. Any one of those would be better party leaders and main characters, than someone whose only experience is 'street urchin'.
Never mind that the aforementioned complaints about lazy script and story writing also apply here, in spades.
And that's where my rant must stop, as 12 put me off the series. Not to mention, not owning a PS3.
Tl;dr, Final Fantasy 6 and to a lesser extent, 7, stand as examples of mostly good story writing, while the others seem to have the Family Guy writing team behind them.