6. The heroes are terrorists
It's easy to hate Shinra because they're literally sucking the lifeforce out of the planet, but the rebel group AVALANCHE isn't much better. For the first few hours of the game, all Cloud does is follow Barret around, blowing up one energy reactor after another. Noble goal or no, the fact remains that Cloud and his friends are domestic terroists.
These reactors weren't in the middle of nowhere. They were directly attached to the biggest city in the world via the slums. AVALANCHE's acts of "heroism" undoubtedly killed scores of the very same people they were trying to liberate.
And that was fine when the game was released in 1997; it was a different time. Back then, terrorism was exciting and Drew Carey was one of People Magazine's Sexiest Men Alive. During that time, these kinds of heinous acts were seen as justifiable in order to make a difference. And then 9/11 happened, and terrorism became a word so scorned that America declared war on it.
Looking back, a Westernized and affluent country being targeted by a small group of bandits hiding in plain sight sounds eerily familiar. This is the kind of thing that's going to be hard to avoid in the impending remake, but some scenes are going to be easier to cut out...
5. Red XIII is introduced by trying to rape Aerith
Nanaki is the team's requisite talking pet/dog/cat/lion thing, though he's most often referred to as Red XIII. Perpetuating the latter name is kind of a messed up thing to do, considering that was Nanaki's name during the time he was a scientific experiment. It's kind of like walking up to John McCain and calling him P.O.W. #3467.
As with most of the beast races in Final Fantasy, the game completely forgets about Red XIII after his moment in the sun (see also: Freya and Kimahri). Even the films and side games neglect Red XIII, probably in part because his fur was too tough to animate.
But maybe we're better off without him; after all, the first time we see Red XIII, he's trying to rape Aerith.
Let's break down what's happening here. The evil scientist Hojo captured Aerith and Red XIII and placed them in the chamber you see front-and-center. Remember, Aerith is the last of an ancient race of humans, and Red XIII is the last of the an ancient race of... lion-cat-dog things. Hojo's whole plan is to breed Aerith and Red XIII together to save both of their species. It's not clear if that's even possible, but mad scientists are not often concerned with biological compatibility.
Fortunately, Cloud and Barret storm in and shoot the place up while the test subject makes a break for freedom. Red XIII quickly whips up an excuse for his actions.
Up to this point, Red certainly seemed game for what was about to happen. Tail wagging, he was absoutely ready to pounce on this human woman. Seeing as he was already in the cage with his intended mating partner, what exactly was Red XIII's plan? Wait for a guy with a gun-arm to start shooting up the place? Would he have gone through with it if Cloud and Barret had not intervened? Thankfully, we'll never have to know, and Red XII's red rocket can stay dormant.