Designated Hero: Julia and Sephiroth perform outright atrocities and genocide, yet they are invariably considered the heroes.
Arguably, the entire series - and the Jenova Possession Theory in general - is to defend Sephiroth, stating that it was not his fault that he went crazy and tried to destroy the world. However, it fails this, by painting Sephiroth as psychopathic, mentally unstable, emotionally dependent on Julia, and outright vindictive and cruel. So instead of having a good man, who snapped under the truth, we have a jerk who wasn't responsible for trying to destroy the world, but willingly commits torture, genocide, and other equally abhorrent crimes.
Draco in Leather Pants: Sephiroth of course. Bonus points for being a character who canonically wears leather pants. The entire story is focused on how wonderful a boyfriend he is, even though he's a rather lousy one, and defending his actions in the game.
Tseng also gets this, but to a lesser degree.
Nightmare Fuel: Julia's cold blooded torture of her female opponents is quite chilling to read. Perhaps even more disturbing is Sephiroth's complete agreement with her heinous acts and their shared perspective that torturing someone and leaving her to bleed to death is nothing more than payback for her breaking Julia's sword.
Nightmare Retardant: Jenova taking over Sephiroth's body and raping Julia and the few other scenes connected to the event are this. Not helped by the fact that Julia gets over the rape in two days and continues as if nothing happened.
Ron the Death Eater: So much. Virtually any hero of the story gets trashed for being opposition to Sephiroth. Primarily we have
Cloud The Idiot: When she actually manages to lock down a personality for Cloud it's a pathetic, wimpy coward who manages to lose his ID card by getting it stuck between his teeth.
Zack The Misogynist: Zack gets turned into a violent, petty, and sexist asshole, who delights in torturing Sephiroth and Julia in anyway he can.
Reno The Prankster: Depending on whether she likes Reno at the moment, Reno is a clumsy, lazy, idiot who is failing every class, and is known for deadly pranks.
Hojo The Sadist: Hojo goes from an ambitious, amoral scientist to a violent psychopath who delights in torturing anybody he can.
Aerith the Friendly Helpful Cheerleader: Special recognition goes to Aerith, who is actually portrayed relatively close to canon. The few scenes she gets she's optimistic, smiling, friendly and helpful. For some reason, everybody hates her, and the audience is supposed to understand why.
Squick: A young Julia (aged around 11-14) is raped by her father as punishment for refusing to have sex with a client, with her mother watching from the treshold. Made much worse by the fact that Julia is an Author Avatar and the evil parents are named after the author's own parents.
Unintentionally Sympathetic: It's hard not to feel sorry for Cloud, as he is bullied and demeaned in every scene that he is in. Julia shoots a marble at his eye for no other reason than he was asleep before class, Reno snaps at him when he was trying to defuse a tense situation, sneakily cuts off so much of his hair that Cloud is left with a bald spot and leaves the cafeteria crying, and when Cloud is forced to join the military, Reno mocks his name, calls him an idiot and pulls the keycard that Cloud had somehow gotten stuck between his teeth so hard that it leaves a large gap. Nothing Cloud ever did or said invited such callous treatment. Cloud is openly hated by both the characters and the author, who obviously did not intend for him to appear as anything but pathetic.
Despite being nice and friendly, Aerith Gainsborough receives the same treatment from the other characters and the author. She is bullied twice by Reno by having ink splashed all over her, one time at school and the other time during homecoming and has other characters call her ugly and be exasperated with her for no discernable reason at all. In fact, when Rude finds out that she'll be in a play, he says he won't waste money to see it. Their negative attitudes are never explained through anything but the author's own virulent dislike of her. In the one scene she has where she actually does anything and has lines, she is warm and friendly to Sephiroth, helping him pick out the best flowers to give to Julia at the hospital. Despite being nothing but helpful, the moment they leave, Sephiroth berates Yuffie for forcing him to spend time with Aerith and acts like the entire experience was pure torture.
The people of Wutai could fit this trope. They declare war on Shinra but don't actually do anything to harm them, and Shinra sends Sephiroth and Julia, huge fans of the Final Solution. They order the army to decimate every settlement they come across and eventually kill millions by summoning Bahamut to wipe out the capital. From start to finish, Shinra is seen as the agressor, and Wutai does nothing but try to defend itself. Also counts as Plot Hole, since the Wutai capital alone had two million ninjas, while the entire Shinra army had barely a hundred thousand people.
Wangst: Julia will go into full on depression when the story is lacking drama. Often on things that happened years ago.
What an Idiot: Despite both of them earning a lot of money, Sephiroth and Julia chose to live for five years with the insane, abusive professor Hojo instead of moving out and finding a place of their own.
Julia staying with her abusive biological family (two unenhanced, normal humans), even though she was apparently very skilled at combat (having taught basic combat to herself) and possessing several materia such as Bolt and Choco Mog, which she's had since she was six, meaning that she was an experienced caster. There is no reason why someone like her wouldn't just run away and try to make it back to her foster family in Mideel, where Tseng would have helped her hide in case her biological family came back looking for her.
Julia and Sephiroth's double rape under Jenova's influence could have been averted if Julia had been smart enough to not enter Sephiroth's tent and instead send someone like Korokou to check up on him. Rather than do that, she enters his tent against his specific warnings and knowing that Jenova could take control of him and make him hurt her.
The Woobie: Sephirothslave tries to invoke this with both Sephiroth and Julia, but they are so incredibly unsympathetic and the writing is so bad that instead of making readers pity them, it ends up looking like the characters either deserved their punishment or were stupid enough to get themselves into the situation that led to it.