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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
"Why?" is a J-pop theme, which plays during the game's ending and segues into the end credits. It's easily the standout among the soundtrack, as the vocals (by Ayaka) are awesome and doubles as a Tear Jerkernote especially once you see the english translation of the lyrics and realize the song is essentially from Zack's PoV, telling Cloud it's okay for him to open up a little and let others in.
Most of the game's soundtrack accounts to this, such as some of the remixes of music from FFVII such as "On The Verge of the Assault" which is a remix of Those Who Fight. An epic version is part of the ending credits music.
Also, "The Price of Freedom". Whilst this pops up in one or two cutscenes, this music finds its place in the background of Zack's final battle.
Genesis's boss tunes are quite appropriate for the battles, despite all the heavy metal, or rather, because of it for some.
Demonic Spiders: Take your pick: Wasps that are highly defensive against weapon damage and have insta-death abilities, those blobs that are highly resistant to all damage and are capable of casting spells in the max damage range, or... just see the damn article already. This game has a lot.
The Costly Punch; do 9999 damage each hit regardless of stats or level for the cost of just a few HP! Made worse if you equip the accessory that ups the damage limit to 99999.
With enough time spent using Materia Fusion (expedited significantly if you know what you're doing), you can get Zack's stats to absolute perfect levels, and with the right equipment, make consistently perfect use of them.
Vital Slash, a materia that allows you to do a critical attack that is much more powerful than a normal critical attack. Level it up and it does 9,999 damage pretty much every time, with just a couple seconds' delay. Equip an item or materia that gives Endure, and you can basically just brush off most attacks and smash tougher enemies' faces into the floor in about a second and a half. And if you equip the aforementioned accessory to raise the damage limit...
Hilarious in Hindsight: The significance the three characters who wield it put in the Buster Sword can be this if one remembers how in the original game the first thing you did when you came to a weapons shop was to ditch it and buy a better one.
Ho Yay: Various combinations with Zack, Sephiroth, and/or Angeal.
Narm: The Climax Boss fight with Hollander quickly becomes silly when you behold his cinematic attack — he reaches into his satchel, pulls out a giant missile bigger than him that he has trouble holding, and throws it at Zack. Not that it wasn't already.
The death scene at the end can also qualify. Here, we go from a silent, sudden death to a heroic passing-of-the-torch speech that seems to drag on forever, then a j-pop song plays as Angeal appears to take him off to heaven... in a game-verse where heaven does not exist. Huh.
That's generally interpreted as Zack returning to the Lifestream.
Genesis, largely for the fact he spends a lot of the time he's on-screen reciting bad poetry. There is also the small problem of him being a self-centered asshole, who directly and indirectly causes every tragedy that happened in the game (And several in Final Fantasy VII to boot), in an attempt to remove an ailment which was his own fault to begin with, while the plot attempts to treat him as The Woobie.
Angeal gets this in some circles for the Drinking Game focused on him constantly using the words "honor" and "dreams" in pretty much every other line of dialogue he has. Even Sephiroth mocks him for it at one point.
And no one, even in-universe, likes Dr. Hollander.
Squick: Sephiroth's fanclub, the "Silver Elite" is headed by a mysterious "Chairwoman H." The game implies this is Hojo. Okay, he's the head of Sephiroth's fanclub, not so bad... until you read the email where he informs the club members of what Sephiroth uses to wash his hair, including rose and vanilla-scented perfumes, and says he goes through a bottle of conditioner every wash. Get your Brain Bleach ready—first, think about the possible ways Hojo could know Sephiroth's bathing habits. Second, think about why he would want to know. Hair care isn't exactly pivotal to scientific research... Then remember that Hojo is, in fact, Sephiroth's dad.
The game could easily have gone more in-depth on Zack and Cloud's time as friends under Shinra, and focused on the Wutai War, the Turks and Aerith. There was no real need to introduce Genesis or to center the plot so heavily around him, especially since he ended up being a ScrappyVillain Sue and generally one of the least liked things about the game.
Square actually wanted to expand Zack and Cloud's friendship but deadlines stopped them from doing that.
The game contains almost no references to Before Crisis or the events in that game including AVALANCHE, save for fighting them in one mission and Zack visiting the graves of two SOLDIER members from Before Crisis. This is despite the fact that Zack was a prominent supporting character in Before Crisis, the two SOLDIER members whose graves he visits were said to be close comrades of his and fought with him on assignments (they never appear in Crisis Core at all) and Cissnei is actually one of the playable Turks of Before Crisis. According to the official timeline the games run parallel with each other, meaning Shinra is fighting two wars at once, AVALANCHE and the Genesis Army, yet you barely hear even whispers of the former.
Unintentionally Unsympathetic: The game wants you to feel sorry for Genesis, who is suffering a genetically degrading disease and is so desperate for a cure he's allowing Hollander and Lazard to use him. Except he's an arrogant, long-winded jerk, the injury that triggered the disease is his own fault, and oh yes, you could make a strong case that if he hadn't started his rebellion against Shinra, the events that set Sephiroth's Start of Darkness in motion might not have happened.
Villain Sue: Genesis. Powers to rival Sephiroth's, an outfit and weapon that essentially are exactly the same as his except red, but unlike Sephiroth he's meant to be a sympathetic character who just wants to heal himself and regain his pride. Ultimately he's a Karma Houdini who is cured of his degredation and survives the game's ending, and to top it all off is admitted to be an Ink-Suit Actor for the pop star Geckt of who Nomura is a fan. According to Word of God, he even pulled a Heel-Face Turn in a later installment of the series, namely when he refused to help Deepground (who are much, much worse than he is). As a whole, Genesis's bio reads like someone's self-insert character, "just like Sephiroth, but cooler and a good guy".